f = open('et.inp', 'w')
f.write(""" $CONTRL COORD=ZMT UNITS=ANGS dfttyp=b3lyp RUNTYP=ENERGY $END
$BASIS GBASIS=N31 NGAUSS=6
POLAR=POPN31 NDFUNC=1 $END
$GUESS GUESS=HUCKEL $END
$system mwords=2 $end
$DATA
eth
C1
C
C 1 cc
H 2 ch 1 cchv
H 2 ch 1 cch 3 d1 0
H 2 ch 1 cch 3 d2 0
H 1 ch 2 cch 3 d3 0
H 1 ch 2 cch 5 d3 0
H 1 chv 2 cch 4 d3 0
cc=1.52986
ch=1.08439
chv=1.08439
cch=111.200
cchv=111.200
d1=120
d2=-120
d3=180
$END""")
f.close()
%%bash
for i in {-10..10}; do
nb=$(echo "scale=5; 1.52986 + $i/50" | bc -l)
sed "s/cc=1.52986/cc=$nb/" et.inp > b_${i}.inp
done
%%bash
rm -rf ~/gamess-scratch/
for i in {-10..10}; do
gms b_${i}.inp 1 > b_${i}.log
done
%%bash
for i in {-10..10}; do
nb=$(echo "scale=5; 1.52986 + $i/50" | bc -l)
echo -n "$nb "
#awk '/TOTAL ENERGY =/{print $4}' b_${i}.log | tail -n 1
awk '/TOTAL ENERGY =/{print $4}' b_${i}.log
done
1.32986 -79.7339315289 1.34986 -79.7406173737 1.36986 -79.7462868578 1.38986 -79.7510331813 1.40986 -79.7549412921 1.42986 -79.7580886263 1.44986 -79.7605457819 1.46986 -79.7623771323 1.48986 -79.7636413832 1.50986 -79.7643920816 1.52986 -79.7646780790 1.54986 -79.7645439543 1.56986 -79.7640303992 1.58986 -79.7631745699 1.60986 -79.7620104053 1.62986 -79.7605689179 1.64986 -79.7588784564 1.66986 -79.7569649422 1.68986 -79.7548520851 1.70986 -79.7525615748 1.72986 -79.7501132582
%%bash
rm bond
for i in {-10..10}; do
nb=$(echo "scale=5; 1.52986 + $i/50" | bc -l)
echo -n "$nb " >> bond
awk '/TOTAL ENERGY =/{print $4}' b_${i}.log >> bond
done
import numpy as np
import matplotlib.pyplot as plt
from scipy import optimize
a = np.loadtxt("bond")
x_o=a[:,0]
y_o=a[:,1]
print "Initial data:", y_o
#function is f(x)=k(b-x)^2 + a
fitfunc = lambda p, x: p[0]*pow(p[1]-x,2) + p[2] # Target function
errfunc = lambda p, x, y: fitfunc(p, x) - y # Error function
p0 = [1,1, -79] # Initial guess for the parameters
p1, success = optimize.leastsq(errfunc, p0[:], args=(x_o, y_o))
print "Optimized params:", p1
#Plot it
plt.plot(x_o, y_o, "ro", x_o,fitfunc(p1,x_o),"r-",c='blue',alpha=0.5)
plt.xlim(1.3,1.8)
plt.savefig('bond.png')
plt.show()
Initial data: [-79.73393153 -79.74061737 -79.74628686 -79.75103318 -79.75494129 -79.75808863 -79.76054578 -79.76237713 -79.76364138 -79.76439208 -79.76467808 -79.76454395 -79.7640304 -79.76317457 -79.76201041 -79.76056892 -79.75887846 -79.75696494 -79.75485209 -79.75256157 -79.75011326] Optimized params: [ 0.56360732 1.55431773 -79.76518585]
%%bash
export PATH=${PATH}:/home/preps/golovin/progs/bin
babel -igamout b_0.log -opdb et.pdb
Ante_RED-1.5.pl et.pdb
**************************************************************************** ** Ante_R.E.D. program (version 1.5) ** ** http://q4md-forcefieldtools.org/RED/ ** ** ** ** Distributed under the GNU General Public License ** ** ** ** Ante_R.E.D. developments were initiated in Prof. D.A. Case's lab. by ** ** R. Lelong,(1,2) P. Cieplak,(3) & F.-Y. Dupradeau (1,2) ** ** ** ** Ante_R.E.D. 1.x were developed in Amiens by ** ** F.-Y. Dupradeau(4) & P. Cieplak,(3) ** ** ** ** Ante_R.E.D. 2.0 is currently developed in Amiens by ** ** G. Klimerak,(4) P. Cieplak(3) & F.-Y. Dupradeau(4) ** **************************************************************************** ** (1) DMAG EA-3901 & Faculte de Pharmacie, UPJV, Amiens, France ** ** (2) The Scripps Research Institute, La Jolla, CA, USA ** ** (3) Sanford|Burnham Institute for Medical Research, La Jolla, CA, USA ** ** (4) UMR CNRS 6219 & UFR de Pharmacie, UPJV, Amiens, France ** **************************************************************************** Replace atom names by names used by R.E.D.-III.x/IV... [Done] Use 'CT' for C atoms connected to 2 or 3 H atoms... [Done] Add a number to each new atom name... [Done] Sort atoms by numbers... [Done] Sort atoms by atom names... [Done] Establish new connectivities between atoms... [Done] Create the P2N output file: et-out.p2n... [Done] Create a new PDB output file: et-out.pdb... [Done] Create a GAMESS-US input file: et-gam.inp... [Done] Create a PC-GAMESS input file: et-pcg.inp... [Done] Create a GAUSSIAN input file: et-gau.com... [Done] Create the information output file: et-info.txt... [Done] QM program inputs generated by Ante_R.E.D. only provides starting points: They should be manually adapted to consider the specificity of each case... **************************************************************************** ** Do you need a new feature which is not yet implemented in Ante_R.E.D.? ** ** contact the q4md force field tools team @ ** ** contact@q4md-forcefieldtools.org ** ** Regularly look for bug fixes at the R.E.D. Home Page ** ** ---- ** ** Visit R.E.D. Server @ http://q4md-forcefieldtools.org/REDS/ as well ** ** ---- ** ** Please, submit your force field library(ies) to R.E.DD.B. @ ** ** http://q4md-forcefieldtools.org/REDDB/ ** ** to freely share your results with the scientific community ** ** ---- ** ** Do you need help about the q4md force field tools? ** ** Please, use the q4md-forcefieldtools.org mailing list @ ** ** http://lists.q4md-forcefieldtools.org/ ** **************************************************************************** ** We thank you for using Ante_R.E.D. ** ****************************************************************************
1 molecule converted 12 audit log messages
%%bash
export PATH=${PATH}:/home/preps/golovin/progs/bin
rm /home/students/y12/popov/gamess-scratch/*
cp et-out.p2n Mol_red1.p2n
RED-vIII.51.pl
---------------------------
* Welcome to R.E.D. III.51 *
RESP ESP charge Derive
http://q4md-forcefieldtools.org/RED/
CHARGE TYPE = RESP-A1
---------------------------
Distributed under the GNU General Public License
---------------------------
Date: Thu Mar 24 16:12:56 MSK 2016
Machine: kodomo.fbb.msu.ru
---------------------------
Number of cpu(s) used in the QM jobs(s): 1
---------------------------
* Operating system *
Linux kodomo.fbb.msu.ru 3.8-2-amd64 #1 SMP Debian 3.8.13-1 x86_64 GNU/Linux
DID YOU PREPARE YOUR P2N INPUT FILES USING ANTE_R.E.D. 2.0/R.E.D SERVER?
WE STRONGLY RECOMMAND YOU TO USE ANTE_R.E.D. 2.0/R.E.D SERVER TO PREPARE YOUR P2N FILES...
Charge correction will be carried out at 1.10-4 e.
===========================================================================
======================= Single molecule ===========================
The molecule TITLE is "MOLECULE"
The TOTAL CHARGE value of the molecule is "0"
The SPIN MULTIPLICITY value of the molecule is "1"
===========================================================================
* 1 conformation(s) selected *
WARNING:
A 2nd column of atom names is detected
This 2nd column will be used in the PDB (& Tripos) file(s)
WARNING:
No three atom based re-orientation found in the P2N file
Re-orientation will be done according to the GAMESS Algorithm!
* Selected QM Software *
GAMESS
* Software checking *
gamess.00.x [ OK ]
rungms [ OK ]
ddikick.x [ OK ]
resp [ OK ]
The Scratch directory defined for GAMESS is /home/students/y12/popov/gamess-scratch
Scratch directory for GAMESS [ OK ]
The punch file directory defined for GAMESS is $SCR/$JOB.dat
Geometry optimization(s) is/are being computed for molecule 1 ... [ OK ]
See the file(s) "JOB1-gam_m1-1.log"
MEP(s) is/are being computed for molecule 1 ... [ OK ]
See the file(s) "JOB2-gam_m1-1-(X).log"
The RESP-A1 charges are being derived for molecule 1 ... [ OK ]
See the "punch2_m1" file(s)
The following Tripos mol2 file(s) has/have been created.
Mol_m1-o1.mol2
Charge values & force field libraries are available in
the "Data-RED" directory.
Execution time: 0 h 0 m 15 s
*************************************************************************
R.E.D. I was developed @ the "Faculte de Pharmacie" in Amiens by:
A.Pigache,(1) P.Cieplak(2) & F.-Y.Dupradeau(1)
R.E.D. II was developed in D.A.Case's laboratory at "TSRI" by:
T.Zaffran,(1,3) P.Cieplak(2) & F.-Y.Dupradeau(1,3)
R.E.D. III.x developments were initiated in D.A.Case's laboratory @ TSRI
& are now carried out @ the "UFR de Pharmacie" in Amiens by:
F.Wang,(5) E.Garcia,(5) N.Grivel,(1,3) P.Cieplak(4) & F.-Y.Dupradeau(1,3,5)
R.E.D. IV is developed @ the "UFR de Pharmacie" in Amiens by:
F.Wang,(5) W.Rozanski,(5) E.Garcia,(5) D.Lelong,(5) P.Cieplak(4)
& F.-Y.Dupradeau(5)
(1) DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
(2) Accelrys Inc., San Diego, USA
(3) D.A.Case's lab., The Scripps Research Institute, La Jolla, CA, USA
(4) Sanford|Burnham Institute for Medical Research, La Jolla, CA, USA
(5) CNRS UMR 6219 & UFR de Pharmacie, Amiens, France
*************************************************************************
R.E.D. III.5 is distributed under the GNU General Public License
*************************************************************************
Do you need a new feature which is not yet implemented in R.E.D.-III.5?
contact the q4md force field tools team @
contact@q4md-forcefieldtools.org
Regularly look for bug fixes at the R.E.D. home page
To use R.E.D. IV, see R.E.D. Server @
http://q4md-forcefieldtools.org/REDS/
----
Please, submit your force field library(ies) to R.E.DD.B. @
http://q4md-forcefieldtools.org/REDDB/
to freely review & share your results within the scientific community
----
Do you need help about the q4md force field tools?
Please, use the q4md-forcefieldtools.org mailing list @
http://lists.q4md-forcefieldtools.org/
*************************************************************************
%%bash
grep "<TRIPOS>ATOM" Data-RED/Mol_m1-o1.mol2 -A 8
@<TRIPOS>ATOM 1 C 0.763688 0.000000 -0.000000 C 1 LIG -0.0190 **** 2 H 1.156406 0.000000 -1.012074 H 1 LIG 0.0059 **** 3 H 1.156406 0.876482 0.506037 H 1 LIG 0.0059 **** 4 H 1.156406 -0.876482 0.506037 H 1 LIG 0.0059 **** 5 C -0.763688 0.000000 0.000000 C 1 LIG -0.0155 **** 6 H -1.156406 0.000000 1.012074 H 1 LIG 0.0056 **** 7 H -1.156406 0.876482 -0.506037 H 1 LIG 0.0056 **** 8 H -1.156406 -0.876482 -0.506037 H 1 LIG 0.0056 ****
%%bash
grep "TOTAL MULLIKEN" Data-RED/JOB2-gam_m1-1-1.log -A 9
TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS
ATOM MULL.POP. CHARGE LOW.POP. CHARGE
1 C 6.475593 -0.475593 6.442144 -0.442144
2 H 0.841469 0.158531 0.853681 0.146319
3 H 0.841469 0.158531 0.852088 0.147912
4 H 0.841469 0.158531 0.852088 0.147912
5 C 6.475593 -0.475593 6.442144 -0.442144
6 H 0.841469 0.158531 0.853681 0.146319
7 H 0.841469 0.158531 0.852088 0.147912
8 H 0.841469 0.158531 0.852088 0.147912
%%bash
echo "[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333" > et.top
%%bash
echo "[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
H 1 1.008 0.0000 A 1.06908e-01 1.00000e-00
C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01" >> et.top
%%bash
echo "[ moleculetype ]
; Name nrexcl
et 3" >> et.top
%%bash
echo "[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 C 1 ETH C1 1 -0.10 12.01
2 C 1 ETH C2 2 -0.10 12.01
3 H 1 ETH H1 3 0.0 1.008
4 H 1 ETH H2 4 0.0 1.008
5 H 1 ETH H3 5 0.0 1.008
6 H 1 ETH H4 6 0.0 1.008
7 H 1 ETH H5 7 0.0 1.008
8 H 1 ETH H6 8 0.0 1.008" >> et.top
%%bash
echo "[ bonds ]
; ai aj funct b0 kb
1 2 1 0.1525 250000.0
1 3 1 0.1085 300000.0
1 4 1 0.1085 300000.0
1 5 1 0.1085 300000.0
2 6 1 0.1085 300000.0
2 7 1 0.1085 300000.0
2 8 1 0.1085 300000.0" >> et.top
%%bash
echo "[ angles ]
; ai aj ak funct phi0 kphi
;around c1
3 1 4 1 109.500 200.400
4 1 5 1 109.500 200.400
3 1 5 1 109.500 200.400
2 1 3 1 109.500 200.400
2 1 4 1 109.500 200.400
2 1 5 1 109.500 200.400
;around c2
1 2 6 1 109.500 400.400
6 2 8 1 109.500 200.400
6 2 7 1 109.500 200.400
7 2 8 1 109.500 200.400
1 2 7 1 109.500 200.400
1 2 8 1 109.500 200.400" >> et.top
%%bash
echo "[ dihedrals ]
; ai aj ak al funct t0 kt mult
3 1 2 6 1 0.0 0.62760 3
3 1 2 7 1 0.0 0.62760 3
3 1 2 8 1 0.0 0.62760 3
4 1 2 6 1 0.0 0.62760 3
4 1 2 7 1 0.0 0.62760 3
4 1 2 8 1 0.0 0.62760 3
5 1 2 6 1 0.0 0.62760 3
5 1 2 7 1 0.0 0.62760 3
5 1 2 8 1 0.0 0.62760 3" >> et.top
%%bash
echo "[ pairs ]
; ai aj funct
3 6
3 7
3 8
4 6
4 7
4 8
5 6
5 7
5 8" >> et.top
%%bash
echo "[ System ]
; any text here
first one
[ molecules ]
;Name count
et 38" >> et.top
%%bash
for i in {1..7};do
ep=$( echo "scale=5; 1/$i/$i/$i" | bc -l )
sed "s/1.00000e-00/$ep/" et.top > v_${i}.top
done
%%bash
for i in {1..7};do
ep=$( echo "scale=5; 1/$i/$i/$i" | bc -l )
grompp_d -f md -c box_big -p v_${i}.top -o vb_${i} -maxwarn 1 && mdrun_d -deffnm vb_${i} -v
grompp_d -f md -c box_38 -p v_${i}.top -o v_${i} -maxwarn 1 && mdrun_d -deffnm v_${i} -v
done
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Glycine aRginine prOline Methionine Alanine Cystine Serine
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_d (double precision) (-:
turning all bonds into constraints...
Analysing residue names:
There are: 38 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 20 Mb of data
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_big.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_1.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o vb_1.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_1.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#93: "Pretend That You're Hercule Poirot" (TeX)
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s vb_1.tpr Input Run input file: tpr tpb tpa
-o vb_1.trr Output Full precision trajectory: trr trj cpt
-x vb_1.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vb_1.cpt Input, Opt. Checkpoint file
-cpo vb_1.cpt Output, Opt. Checkpoint file
-c vb_1.gro Output Structure file: gro g96 pdb etc.
-e vb_1.edr Output Energy file
-g vb_1.log Output Log file
-dhdl vb_1.xvg Output, Opt. xvgr/xmgr file
-field vb_1.xvg Output, Opt. xvgr/xmgr file
-table vb_1.xvg Input, Opt. xvgr/xmgr file
-tablep vb_1.xvg Input, Opt. xvgr/xmgr file
-tableb vb_1.xvg Input, Opt. xvgr/xmgr file
-rerun vb_1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vb_1.xvg Output, Opt. xvgr/xmgr file
-tpid vb_1.xvg Output, Opt. xvgr/xmgr file
-ei vb_1.edi Input, Opt. ED sampling input
-eo vb_1.edo Output, Opt. ED sampling output
-j vb_1.gct Input, Opt. General coupling stuff
-jo vb_1.gct Output, Opt. General coupling stuff
-ffout vb_1.xvg Output, Opt. xvgr/xmgr file
-devout vb_1.xvg Output, Opt. xvgr/xmgr file
-runav vb_1.xvg Output, Opt. xvgr/xmgr file
-px vb_1.xvg Output, Opt. xvgr/xmgr file
-pf vb_1.xvg Output, Opt. xvgr/xmgr file
-mtx vb_1.mtx Output, Opt. Hessian matrix
-dn vb_1.ndx Output, Opt. Index file
-multidir vb_1 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vb_1 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vb_1.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.237 25.237 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.977 171.181 0.140
gcq#154: "Right Between the Eyes" (F. Zappa)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_38.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_1.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o v_1.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.15#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_1.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#154: "Right Between the Eyes" (F. Zappa)
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s v_1.tpr Input Run input file: tpr tpb tpa
-o v_1.trr Output Full precision trajectory: trr trj cpt
-x v_1.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi v_1.cpt Input, Opt. Checkpoint file
-cpo v_1.cpt Output, Opt. Checkpoint file
-c v_1.gro Output Structure file: gro g96 pdb etc.
-e v_1.edr Output Energy file
-g v_1.log Output Log file
-dhdl v_1.xvg Output, Opt. xvgr/xmgr file
-field v_1.xvg Output, Opt. xvgr/xmgr file
-table v_1.xvg Input, Opt. xvgr/xmgr file
-tablep v_1.xvg Input, Opt. xvgr/xmgr file
-tableb v_1.xvg Input, Opt. xvgr/xmgr file
-rerun v_1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi v_1.xvg Output, Opt. xvgr/xmgr file
-tpid v_1.xvg Output, Opt. xvgr/xmgr file
-ei v_1.edi Input, Opt. ED sampling input
-eo v_1.edo Output, Opt. ED sampling output
-j v_1.gct Input, Opt. General coupling stuff
-jo v_1.gct Output, Opt. General coupling stuff
-ffout v_1.xvg Output, Opt. xvgr/xmgr file
-devout v_1.xvg Output, Opt. xvgr/xmgr file
-runav v_1.xvg Output, Opt. xvgr/xmgr file
-px v_1.xvg Output, Opt. xvgr/xmgr file
-pf v_1.xvg Output, Opt. xvgr/xmgr file
-mtx v_1.mtx Output, Opt. Hessian matrix
-dn v_1.ndx Output, Opt. Index file
-multidir v_1 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string v_1 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file v_1.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.126 25.126 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.994 171.939 0.140
gcq#101: "My Heart is Just a Muscle In a Cavity" (F. Black)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_big.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_2.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o vb_2.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_2.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#101: "My Heart is Just a Muscle In a Cavity" (F. Black)
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s vb_2.tpr Input Run input file: tpr tpb tpa
-o vb_2.trr Output Full precision trajectory: trr trj cpt
-x vb_2.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vb_2.cpt Input, Opt. Checkpoint file
-cpo vb_2.cpt Output, Opt. Checkpoint file
-c vb_2.gro Output Structure file: gro g96 pdb etc.
-e vb_2.edr Output Energy file
-g vb_2.log Output Log file
-dhdl vb_2.xvg Output, Opt. xvgr/xmgr file
-field vb_2.xvg Output, Opt. xvgr/xmgr file
-table vb_2.xvg Input, Opt. xvgr/xmgr file
-tablep vb_2.xvg Input, Opt. xvgr/xmgr file
-tableb vb_2.xvg Input, Opt. xvgr/xmgr file
-rerun vb_2.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vb_2.xvg Output, Opt. xvgr/xmgr file
-tpid vb_2.xvg Output, Opt. xvgr/xmgr file
-ei vb_2.edi Input, Opt. ED sampling input
-eo vb_2.edo Output, Opt. ED sampling output
-j vb_2.gct Input, Opt. General coupling stuff
-jo vb_2.gct Output, Opt. General coupling stuff
-ffout vb_2.xvg Output, Opt. xvgr/xmgr file
-devout vb_2.xvg Output, Opt. xvgr/xmgr file
-runav vb_2.xvg Output, Opt. xvgr/xmgr file
-px vb_2.xvg Output, Opt. xvgr/xmgr file
-pf vb_2.xvg Output, Opt. xvgr/xmgr file
-mtx vb_2.mtx Output, Opt. Hessian matrix
-dn vb_2.ndx Output, Opt. Index file
-multidir vb_2 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vb_2 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vb_2.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.208 25.208 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.981 171.377 0.140
gcq#47: "I Am Testing Your Grey Matter" (Red Hot Chili Peppers)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_38.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_2.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o v_2.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_2.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#47: "I Am Testing Your Grey Matter" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s v_2.tpr Input Run input file: tpr tpb tpa
-o v_2.trr Output Full precision trajectory: trr trj cpt
-x v_2.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi v_2.cpt Input, Opt. Checkpoint file
-cpo v_2.cpt Output, Opt. Checkpoint file
-c v_2.gro Output Structure file: gro g96 pdb etc.
-e v_2.edr Output Energy file
-g v_2.log Output Log file
-dhdl v_2.xvg Output, Opt. xvgr/xmgr file
-field v_2.xvg Output, Opt. xvgr/xmgr file
-table v_2.xvg Input, Opt. xvgr/xmgr file
-tablep v_2.xvg Input, Opt. xvgr/xmgr file
-tableb v_2.xvg Input, Opt. xvgr/xmgr file
-rerun v_2.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi v_2.xvg Output, Opt. xvgr/xmgr file
-tpid v_2.xvg Output, Opt. xvgr/xmgr file
-ei v_2.edi Input, Opt. ED sampling input
-eo v_2.edo Output, Opt. ED sampling output
-j v_2.gct Input, Opt. General coupling stuff
-jo v_2.gct Output, Opt. General coupling stuff
-ffout v_2.xvg Output, Opt. xvgr/xmgr file
-devout v_2.xvg Output, Opt. xvgr/xmgr file
-runav v_2.xvg Output, Opt. xvgr/xmgr file
-px v_2.xvg Output, Opt. xvgr/xmgr file
-pf v_2.xvg Output, Opt. xvgr/xmgr file
-mtx v_2.mtx Output, Opt. Hessian matrix
-dn v_2.ndx Output, Opt. Index file
-multidir v_2 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string v_2 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file v_2.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.016 25.016 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 4.012 172.692 0.139
gcq#360: "There's no way you can rely on an experiment" (Gerrit Groenhof)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_big.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_3.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o vb_3.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_3.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#360: "There's no way you can rely on an experiment" (Gerrit Groenhof)
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s vb_3.tpr Input Run input file: tpr tpb tpa
-o vb_3.trr Output Full precision trajectory: trr trj cpt
-x vb_3.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vb_3.cpt Input, Opt. Checkpoint file
-cpo vb_3.cpt Output, Opt. Checkpoint file
-c vb_3.gro Output Structure file: gro g96 pdb etc.
-e vb_3.edr Output Energy file
-g vb_3.log Output Log file
-dhdl vb_3.xvg Output, Opt. xvgr/xmgr file
-field vb_3.xvg Output, Opt. xvgr/xmgr file
-table vb_3.xvg Input, Opt. xvgr/xmgr file
-tablep vb_3.xvg Input, Opt. xvgr/xmgr file
-tableb vb_3.xvg Input, Opt. xvgr/xmgr file
-rerun vb_3.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vb_3.xvg Output, Opt. xvgr/xmgr file
-tpid vb_3.xvg Output, Opt. xvgr/xmgr file
-ei vb_3.edi Input, Opt. ED sampling input
-eo vb_3.edo Output, Opt. ED sampling output
-j vb_3.gct Input, Opt. General coupling stuff
-jo vb_3.gct Output, Opt. General coupling stuff
-ffout vb_3.xvg Output, Opt. xvgr/xmgr file
-devout vb_3.xvg Output, Opt. xvgr/xmgr file
-runav vb_3.xvg Output, Opt. xvgr/xmgr file
-px vb_3.xvg Output, Opt. xvgr/xmgr file
-pf vb_3.xvg Output, Opt. xvgr/xmgr file
-mtx vb_3.mtx Output, Opt. Hessian matrix
-dn vb_3.ndx Output, Opt. Index file
-multidir vb_3 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vb_3 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vb_3.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.068 25.068 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 4.003 172.334 0.139
gcq#306: "Read me your scripture and I will twist it" (Red Hot Chili Peppers)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_38.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_3.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o v_3.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.19#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_3.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#306: "Read me your scripture and I will twist it" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s v_3.tpr Input Run input file: tpr tpb tpa
-o v_3.trr Output Full precision trajectory: trr trj cpt
-x v_3.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi v_3.cpt Input, Opt. Checkpoint file
-cpo v_3.cpt Output, Opt. Checkpoint file
-c v_3.gro Output Structure file: gro g96 pdb etc.
-e v_3.edr Output Energy file
-g v_3.log Output Log file
-dhdl v_3.xvg Output, Opt. xvgr/xmgr file
-field v_3.xvg Output, Opt. xvgr/xmgr file
-table v_3.xvg Input, Opt. xvgr/xmgr file
-tablep v_3.xvg Input, Opt. xvgr/xmgr file
-tableb v_3.xvg Input, Opt. xvgr/xmgr file
-rerun v_3.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi v_3.xvg Output, Opt. xvgr/xmgr file
-tpid v_3.xvg Output, Opt. xvgr/xmgr file
-ei v_3.edi Input, Opt. ED sampling input
-eo v_3.edo Output, Opt. ED sampling output
-j v_3.gct Input, Opt. General coupling stuff
-jo v_3.gct Output, Opt. General coupling stuff
-ffout v_3.xvg Output, Opt. xvgr/xmgr file
-devout v_3.xvg Output, Opt. xvgr/xmgr file
-runav v_3.xvg Output, Opt. xvgr/xmgr file
-px v_3.xvg Output, Opt. xvgr/xmgr file
-pf v_3.xvg Output, Opt. xvgr/xmgr file
-mtx v_3.mtx Output, Opt. Hessian matrix
-dn v_3.ndx Output, Opt. Index file
-multidir v_3 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string v_3 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file v_3.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.137 25.137 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.992 171.863 0.140
gcq#2: "Jesus Built My Hotrod" (Ministry)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_big.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_4.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o vb_4.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_4.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#2: "Jesus Built My Hotrod" (Ministry)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s vb_4.tpr Input Run input file: tpr tpb tpa
-o vb_4.trr Output Full precision trajectory: trr trj cpt
-x vb_4.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vb_4.cpt Input, Opt. Checkpoint file
-cpo vb_4.cpt Output, Opt. Checkpoint file
-c vb_4.gro Output Structure file: gro g96 pdb etc.
-e vb_4.edr Output Energy file
-g vb_4.log Output Log file
-dhdl vb_4.xvg Output, Opt. xvgr/xmgr file
-field vb_4.xvg Output, Opt. xvgr/xmgr file
-table vb_4.xvg Input, Opt. xvgr/xmgr file
-tablep vb_4.xvg Input, Opt. xvgr/xmgr file
-tableb vb_4.xvg Input, Opt. xvgr/xmgr file
-rerun vb_4.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vb_4.xvg Output, Opt. xvgr/xmgr file
-tpid vb_4.xvg Output, Opt. xvgr/xmgr file
-ei vb_4.edi Input, Opt. ED sampling input
-eo vb_4.edo Output, Opt. ED sampling output
-j vb_4.gct Input, Opt. General coupling stuff
-jo vb_4.gct Output, Opt. General coupling stuff
-ffout vb_4.xvg Output, Opt. xvgr/xmgr file
-devout vb_4.xvg Output, Opt. xvgr/xmgr file
-runav vb_4.xvg Output, Opt. xvgr/xmgr file
-px vb_4.xvg Output, Opt. xvgr/xmgr file
-pf vb_4.xvg Output, Opt. xvgr/xmgr file
-mtx vb_4.mtx Output, Opt. Hessian matrix
-dn vb_4.ndx Output, Opt. Index file
-multidir vb_4 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vb_4 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vb_4.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.201 25.201 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.982 171.428 0.140
gcq#315: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_38.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_4.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o v_4.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.21#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_4.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#315: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)
:-) G R O M A C S (-:
Glycine aRginine prOline Methionine Alanine Cystine Serine
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s v_4.tpr Input Run input file: tpr tpb tpa
-o v_4.trr Output Full precision trajectory: trr trj cpt
-x v_4.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi v_4.cpt Input, Opt. Checkpoint file
-cpo v_4.cpt Output, Opt. Checkpoint file
-c v_4.gro Output Structure file: gro g96 pdb etc.
-e v_4.edr Output Energy file
-g v_4.log Output Log file
-dhdl v_4.xvg Output, Opt. xvgr/xmgr file
-field v_4.xvg Output, Opt. xvgr/xmgr file
-table v_4.xvg Input, Opt. xvgr/xmgr file
-tablep v_4.xvg Input, Opt. xvgr/xmgr file
-tableb v_4.xvg Input, Opt. xvgr/xmgr file
-rerun v_4.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi v_4.xvg Output, Opt. xvgr/xmgr file
-tpid v_4.xvg Output, Opt. xvgr/xmgr file
-ei v_4.edi Input, Opt. ED sampling input
-eo v_4.edo Output, Opt. ED sampling output
-j v_4.gct Input, Opt. General coupling stuff
-jo v_4.gct Output, Opt. General coupling stuff
-ffout v_4.xvg Output, Opt. xvgr/xmgr file
-devout v_4.xvg Output, Opt. xvgr/xmgr file
-runav v_4.xvg Output, Opt. xvgr/xmgr file
-px v_4.xvg Output, Opt. xvgr/xmgr file
-pf v_4.xvg Output, Opt. xvgr/xmgr file
-mtx v_4.mtx Output, Opt. Hessian matrix
-dn v_4.ndx Output, Opt. Index file
-multidir v_4 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string v_4 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file v_4.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.149 25.149 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.990 171.777 0.140
gcq#261: "Live for Liposuction" (Robbie Williams)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_big.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_5.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o vb_5.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_5.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#261: "Live for Liposuction" (Robbie Williams)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s vb_5.tpr Input Run input file: tpr tpb tpa
-o vb_5.trr Output Full precision trajectory: trr trj cpt
-x vb_5.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vb_5.cpt Input, Opt. Checkpoint file
-cpo vb_5.cpt Output, Opt. Checkpoint file
-c vb_5.gro Output Structure file: gro g96 pdb etc.
-e vb_5.edr Output Energy file
-g vb_5.log Output Log file
-dhdl vb_5.xvg Output, Opt. xvgr/xmgr file
-field vb_5.xvg Output, Opt. xvgr/xmgr file
-table vb_5.xvg Input, Opt. xvgr/xmgr file
-tablep vb_5.xvg Input, Opt. xvgr/xmgr file
-tableb vb_5.xvg Input, Opt. xvgr/xmgr file
-rerun vb_5.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vb_5.xvg Output, Opt. xvgr/xmgr file
-tpid vb_5.xvg Output, Opt. xvgr/xmgr file
-ei vb_5.edi Input, Opt. ED sampling input
-eo vb_5.edo Output, Opt. ED sampling output
-j vb_5.gct Input, Opt. General coupling stuff
-jo vb_5.gct Output, Opt. General coupling stuff
-ffout vb_5.xvg Output, Opt. xvgr/xmgr file
-devout vb_5.xvg Output, Opt. xvgr/xmgr file
-runav vb_5.xvg Output, Opt. xvgr/xmgr file
-px vb_5.xvg Output, Opt. xvgr/xmgr file
-pf vb_5.xvg Output, Opt. xvgr/xmgr file
-mtx vb_5.mtx Output, Opt. Hessian matrix
-dn vb_5.ndx Output, Opt. Index file
-multidir vb_5 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vb_5 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vb_5.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.017 25.017 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 4.012 172.689 0.139
gcq#208: "Watch Out Where the Huskies Go" (F. Zappa)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_38.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_5.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o v_5.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.23#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_5.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#208: "Watch Out Where the Huskies Go" (F. Zappa)
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s v_5.tpr Input Run input file: tpr tpb tpa
-o v_5.trr Output Full precision trajectory: trr trj cpt
-x v_5.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi v_5.cpt Input, Opt. Checkpoint file
-cpo v_5.cpt Output, Opt. Checkpoint file
-c v_5.gro Output Structure file: gro g96 pdb etc.
-e v_5.edr Output Energy file
-g v_5.log Output Log file
-dhdl v_5.xvg Output, Opt. xvgr/xmgr file
-field v_5.xvg Output, Opt. xvgr/xmgr file
-table v_5.xvg Input, Opt. xvgr/xmgr file
-tablep v_5.xvg Input, Opt. xvgr/xmgr file
-tableb v_5.xvg Input, Opt. xvgr/xmgr file
-rerun v_5.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi v_5.xvg Output, Opt. xvgr/xmgr file
-tpid v_5.xvg Output, Opt. xvgr/xmgr file
-ei v_5.edi Input, Opt. ED sampling input
-eo v_5.edo Output, Opt. ED sampling output
-j v_5.gct Input, Opt. General coupling stuff
-jo v_5.gct Output, Opt. General coupling stuff
-ffout v_5.xvg Output, Opt. xvgr/xmgr file
-devout v_5.xvg Output, Opt. xvgr/xmgr file
-runav v_5.xvg Output, Opt. xvgr/xmgr file
-px v_5.xvg Output, Opt. xvgr/xmgr file
-pf v_5.xvg Output, Opt. xvgr/xmgr file
-mtx v_5.mtx Output, Opt. Hessian matrix
-dn v_5.ndx Output, Opt. Index file
-multidir v_5 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string v_5 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file v_5.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.198 25.198 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.983 171.446 0.140
gcq#154: "Right Between the Eyes" (F. Zappa)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_big.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_6.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o vb_6.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.24#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_6.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#154: "Right Between the Eyes" (F. Zappa)
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s vb_6.tpr Input Run input file: tpr tpb tpa
-o vb_6.trr Output Full precision trajectory: trr trj cpt
-x vb_6.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vb_6.cpt Input, Opt. Checkpoint file
-cpo vb_6.cpt Output, Opt. Checkpoint file
-c vb_6.gro Output Structure file: gro g96 pdb etc.
-e vb_6.edr Output Energy file
-g vb_6.log Output Log file
-dhdl vb_6.xvg Output, Opt. xvgr/xmgr file
-field vb_6.xvg Output, Opt. xvgr/xmgr file
-table vb_6.xvg Input, Opt. xvgr/xmgr file
-tablep vb_6.xvg Input, Opt. xvgr/xmgr file
-tableb vb_6.xvg Input, Opt. xvgr/xmgr file
-rerun vb_6.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vb_6.xvg Output, Opt. xvgr/xmgr file
-tpid vb_6.xvg Output, Opt. xvgr/xmgr file
-ei vb_6.edi Input, Opt. ED sampling input
-eo vb_6.edo Output, Opt. ED sampling output
-j vb_6.gct Input, Opt. General coupling stuff
-jo vb_6.gct Output, Opt. General coupling stuff
-ffout vb_6.xvg Output, Opt. xvgr/xmgr file
-devout vb_6.xvg Output, Opt. xvgr/xmgr file
-runav vb_6.xvg Output, Opt. xvgr/xmgr file
-px vb_6.xvg Output, Opt. xvgr/xmgr file
-pf vb_6.xvg Output, Opt. xvgr/xmgr file
-mtx vb_6.mtx Output, Opt. Hessian matrix
-dn vb_6.ndx Output, Opt. Index file
-multidir vb_6 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vb_6 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vb_6.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.039 25.039 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 4.008 172.534 0.139
gcq#101: "My Heart is Just a Muscle In a Cavity" (F. Black)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_38.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_6.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o v_6.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.25#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_6.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#101: "My Heart is Just a Muscle In a Cavity" (F. Black)
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s v_6.tpr Input Run input file: tpr tpb tpa
-o v_6.trr Output Full precision trajectory: trr trj cpt
-x v_6.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi v_6.cpt Input, Opt. Checkpoint file
-cpo v_6.cpt Output, Opt. Checkpoint file
-c v_6.gro Output Structure file: gro g96 pdb etc.
-e v_6.edr Output Energy file
-g v_6.log Output Log file
-dhdl v_6.xvg Output, Opt. xvgr/xmgr file
-field v_6.xvg Output, Opt. xvgr/xmgr file
-table v_6.xvg Input, Opt. xvgr/xmgr file
-tablep v_6.xvg Input, Opt. xvgr/xmgr file
-tableb v_6.xvg Input, Opt. xvgr/xmgr file
-rerun v_6.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi v_6.xvg Output, Opt. xvgr/xmgr file
-tpid v_6.xvg Output, Opt. xvgr/xmgr file
-ei v_6.edi Input, Opt. ED sampling input
-eo v_6.edo Output, Opt. ED sampling output
-j v_6.gct Input, Opt. General coupling stuff
-jo v_6.gct Output, Opt. General coupling stuff
-ffout v_6.xvg Output, Opt. xvgr/xmgr file
-devout v_6.xvg Output, Opt. xvgr/xmgr file
-runav v_6.xvg Output, Opt. xvgr/xmgr file
-px v_6.xvg Output, Opt. xvgr/xmgr file
-pf v_6.xvg Output, Opt. xvgr/xmgr file
-mtx v_6.mtx Output, Opt. Hessian matrix
-dn v_6.ndx Output, Opt. Index file
-multidir v_6 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string v_6 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file v_6.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.155 25.155 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 3.990 171.739 0.140
gcq#162: "Confirmed" (Star Trek)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_big.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_7.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o vb_7.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.26#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_7.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#162: "Confirmed" (Star Trek)
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s vb_7.tpr Input Run input file: tpr tpb tpa
-o vb_7.trr Output Full precision trajectory: trr trj cpt
-x vb_7.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vb_7.cpt Input, Opt. Checkpoint file
-cpo vb_7.cpt Output, Opt. Checkpoint file
-c vb_7.gro Output Structure file: gro g96 pdb etc.
-e vb_7.edr Output Energy file
-g vb_7.log Output Log file
-dhdl vb_7.xvg Output, Opt. xvgr/xmgr file
-field vb_7.xvg Output, Opt. xvgr/xmgr file
-table vb_7.xvg Input, Opt. xvgr/xmgr file
-tablep vb_7.xvg Input, Opt. xvgr/xmgr file
-tableb vb_7.xvg Input, Opt. xvgr/xmgr file
-rerun vb_7.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vb_7.xvg Output, Opt. xvgr/xmgr file
-tpid vb_7.xvg Output, Opt. xvgr/xmgr file
-ei vb_7.edi Input, Opt. ED sampling input
-eo vb_7.edo Output, Opt. ED sampling output
-j vb_7.gct Input, Opt. General coupling stuff
-jo vb_7.gct Output, Opt. General coupling stuff
-ffout vb_7.xvg Output, Opt. xvgr/xmgr file
-devout vb_7.xvg Output, Opt. xvgr/xmgr file
-runav vb_7.xvg Output, Opt. xvgr/xmgr file
-px vb_7.xvg Output, Opt. xvgr/xmgr file
-pf vb_7.xvg Output, Opt. xvgr/xmgr file
-mtx vb_7.mtx Output, Opt. Hessian matrix
-dn vb_7.ndx Output, Opt. Index file
-multidir vb_7 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vb_7 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vb_7.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.077 25.077 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 4.002 172.274 0.139
gcq#109: "Ease Myself Into the Body Bag" (P.J. Harvey)
Option Filename Type Description
------------------------------------------------------------
-f md.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c box_38.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p v_7.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o v_7.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.27#
NOTE 1 [file md.mdp]:
Simulating without cut-offs is usually (slightly) faster with nstlist=0,
nstype=simple and particle decomposition
NOTE 2 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 3 [file md.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Generated 3 of the 3 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 4 [file v_7.top, line 73]:
System has non-zero total charge: -7.600000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 643.00
There were 4 notes
gcq#109: "Ease Myself Into the Body Bag" (P.J. Harvey)
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s v_7.tpr Input Run input file: tpr tpb tpa
-o v_7.trr Output Full precision trajectory: trr trj cpt
-x v_7.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi v_7.cpt Input, Opt. Checkpoint file
-cpo v_7.cpt Output, Opt. Checkpoint file
-c v_7.gro Output Structure file: gro g96 pdb etc.
-e v_7.edr Output Energy file
-g v_7.log Output Log file
-dhdl v_7.xvg Output, Opt. xvgr/xmgr file
-field v_7.xvg Output, Opt. xvgr/xmgr file
-table v_7.xvg Input, Opt. xvgr/xmgr file
-tablep v_7.xvg Input, Opt. xvgr/xmgr file
-tableb v_7.xvg Input, Opt. xvgr/xmgr file
-rerun v_7.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi v_7.xvg Output, Opt. xvgr/xmgr file
-tpid v_7.xvg Output, Opt. xvgr/xmgr file
-ei v_7.edi Input, Opt. ED sampling input
-eo v_7.edo Output, Opt. ED sampling output
-j v_7.gct Input, Opt. General coupling stuff
-jo v_7.gct Output, Opt. General coupling stuff
-ffout v_7.xvg Output, Opt. xvgr/xmgr file
-devout v_7.xvg Output, Opt. xvgr/xmgr file
-runav v_7.xvg Output, Opt. xvgr/xmgr file
-px v_7.xvg Output, Opt. xvgr/xmgr file
-pf v_7.xvg Output, Opt. xvgr/xmgr file
-mtx v_7.mtx Output, Opt. Hessian matrix
-dn v_7.ndx Output, Opt. Index file
-multidir v_7 Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string v_7 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file v_7.tpr, VERSION 4.5.5 (double precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 3 threads.
You can use the -nt option to optimize the number of threads.
Starting 3 threads
Loaded with Money
starting mdrun 'first one'
50000 steps, 50.0 ps.
step 49900, remaining runtime: 0 s
Writing final coordinates.
step 50000, remaining runtime: 0 s
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 25.090 25.090 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 4.000 172.181 0.139
gcq#55: "Kissing You is Like Kissing Gravel" (Throwing Muses)
%%bash
trjconv_d -f v_3 -s v_3 -o v_3.pdb
Select group for output
:-) G R O M A C S (-:
GRoups of Organic Molecules in ACtion for Science
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) trjconv_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-f v_3.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o v_3.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s v_3.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-[no]round bool no Round measurements to nearest picosecond
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0 Optional starting point for pbc cluster option
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trajectory file after this time
(ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 If the -sep flag is set, use these many digits
for the file numbers and prepend zeros as needed
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
-[no]conect bool no Add conect records when writing .pdb files.
Useful for visualization of non-standard
molecules, e.g. coarse grained ones
Will write pdb: Protein data bank file
Reading file v_3.tpr, VERSION 4.5.5 (double precision)
Reading file v_3.tpr, VERSION 4.5.5 (double precision)
Group 0 ( System) has 304 elements
Group 1 ( Other) has 304 elements
Group 2 ( ETH) has 304 elements
Select a group:
-------------------------------------------------------
Program trjconv_d, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/index.c, line: 1036
Fatal error:
Cannot read from input
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Check Your Output" (P. Ahlstrom)
%%bash
for i in {1..7};do
ep=$( echo "scale=5; 1/$i/$i/$i" | bc -l )
echo -e "LJ-(SR)\nCoulomb-(SR)\n0" | g_energy -f -b 10 vb_${i} -o eb_${i} > vb_${i}.txt
echo -e "LJ-(SR)\nCoulomb-(SR)\n0" | g_energy -f -b 10 v_${i} -o e_${i} > v_${i}.txt
done
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vb_1.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o eb_1.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vb_1.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#259: "I'm Looking for a New Simulation" (Stone Temple Pilots)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f v_1.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o e_1.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened v_1.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#259: "I'm Looking for a New Simulation" (Stone Temple Pilots)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vb_2.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o eb_2.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vb_2.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#259: "I'm Looking for a New Simulation" (Stone Temple Pilots)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f v_2.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o e_2.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened v_2.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#259: "I'm Looking for a New Simulation" (Stone Temple Pilots)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vb_3.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o eb_3.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vb_3.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#259: "I'm Looking for a New Simulation" (Stone Temple Pilots)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f v_3.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o e_3.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened v_3.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#259: "I'm Looking for a New Simulation" (Stone Temple Pilots)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vb_4.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o eb_4.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vb_4.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#259: "I'm Looking for a New Simulation" (Stone Temple Pilots)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f v_4.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o e_4.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened v_4.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#8: "Don't Push Me, Cause I'm Close to the Edge" (Tricky)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vb_5.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o eb_5.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vb_5.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#8: "Don't Push Me, Cause I'm Close to the Edge" (Tricky)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f v_5.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o e_5.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened v_5.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#8: "Don't Push Me, Cause I'm Close to the Edge" (Tricky)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vb_6.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o eb_6.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vb_6.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#8: "Don't Push Me, Cause I'm Close to the Edge" (Tricky)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f v_6.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o e_6.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened v_6.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#8: "Don't Push Me, Cause I'm Close to the Edge" (Tricky)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vb_7.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o eb_7.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vb_7.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#8: "Don't Push Me, Cause I'm Close to the Edge" (Tricky)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f v_7.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o e_7.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 10 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened v_7.edr as double precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Angle 2 Proper-Dih. 3 LJ-14 4 Coulomb-14
5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Temperature 11 Pressure 12 Constr.-rmsd
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z 35 T-System
Last energy frame read 10000 time 50.000
gcq#8: "Don't Push Me, Cause I'm Close to the Edge" (Tricky)