Изучение работы методов контроля температуры в GROMACS¶
In [1]:
from xmlrpclib import ServerProxy
from IPython.display import Image
import os, sys
In [2]:
from IPython.display import Image
Создание индекс-файла с одной группой из одной молекулы этана.¶
In [5]:
%%bash
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/box_38.gro
make_ndx -f box_38.gro -o 1.ndx
Going to read 0 old index file(s) Analysing residue names: There are: 38 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 304 atoms 1 Other : 304 atoms 2 ETH : 304 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index >
--2016-05-04 19:44:05-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/box_38.gro
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 13727 (13K)
Saving to: `box_38.gro'
0K .......... ... 100% 448M=0s
2016-05-04 19:44:05 (448 MB/s) - `box_38.gro' saved [13727/13727]
:-) G R O M A C S (-:
GRowing Old MAkes el Chrono Sweat
:-) 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.
:-) make_ndx (-:
Option Filename Type Description
------------------------------------------------------------
-f box_38.gro Input, Opt! Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt., Mult. Index file
-o 1.ndx Output Index 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
-natoms int 0 set number of atoms (default: read from
coordinate or index file)
Reading structure file
-------------------------------------------------------
Program make_ndx, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/tools/make_ndx.c, line: 965
Fatal error:
Error reading user input
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Yeah, a Wuzz, Or a Jerk" (F. Black)
в окне putty: 2 & r 1
Создадим gro файл с одной молекулой и зададим ячейку¶
In [8]:
%%bash
#зададим ячейку и расположим молекулу по центру ячейку
editconf -f box_38.gro -o et1.gro -n 1.ndx
editconf -f et1.gro -o et.gro -d 2 -c
Read 304 atoms Volume: 3.375 nm^3, corresponds to roughly 1500 electrons No velocities found Error: No such group 'EDITCONF' Error: No such group '_F' Error: No such group 'ET1.GRO' Selected 1: 'Other'
:-) 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.
:-) editconf (-:
Option Filename Type Description
------------------------------------------------------------
-f box_38.gro Input Structure file: gro g96 pdb tpr etc.
-n 1.ndx Input, Opt! Index file
-o et1.gro Output, Opt! Structure file: gro g96 pdb etc.
-mead mead.pqr Output, Opt. Coordinate file for MEAD
-bf bfact.dat Input, Opt. Generic data 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]w bool no View output .xvg, .xpm, .eps and .pdb files
-[no]ndef bool no Choose output from default index groups
-bt enum triclinic Box type for -box and -d: triclinic, cubic,
dodecahedron or octahedron
-box vector 0 0 0 Box vector lengths (a,b,c)
-angles vector 90 90 90 Angles between the box vectors (bc,ac,ab)
-d real 0 Distance between the solute and the box
-[no]c bool no Center molecule in box (implied by -box and -d)
-center vector 0 0 0 Coordinates of geometrical center
-aligncenter vector 0 0 0 Center of rotation for alignment
-align vector 0 0 0 Align to target vector
-translate vector 0 0 0 Translation
-rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees
-[no]princ bool no Orient molecule(s) along their principal axes
-scale vector 1 1 1 Scaling factor
-density real 1000 Density (g/L) of the output box achieved by
scaling
-[no]pbc bool no Remove the periodicity (make molecule whole again)
-resnr int -1 Renumber residues starting from resnr
-[no]grasp bool no Store the charge of the atom in the B-factor
field and the radius of the atom in the occupancy
field
-rvdw real 0.12 Default Van der Waals radius (in nm) if one can
not be found in the database or if no parameters
are present in the topology file
-[no]sig56 bool no Use rmin/2 (minimum in the Van der Waals
potential) rather than sigma/2
-[no]vdwread bool no Read the Van der Waals radii from the file
vdwradii.dat rather than computing the radii
based on the force field
-[no]atom bool no Force B-factor attachment per atom
-[no]legend bool no Make B-factor legend
-label string A Add chain label for all residues
-[no]conect bool no Add CONECT records to a .pdb file when written.
Can only be done when a topology is present
Select a group for output:
Group 0 ( System) has 304 elements
Group 1 ( Other) has 304 elements
Group 2 ( ETH) has 304 elements
Group 3 ( ETH_&_r_1) has 8 elements
Select a group: Select a group: Select a group: Select a group:
Back Off! I just backed up et1.gro to ./#et1.gro.2#
gcq#309: "Gabba Gabba Hey!" (The Ramones)
Построим файл топологии et.top для этана (информация о типах атомов - из /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp)¶
In [17]:
%%bash
echo '#include "/usr/share/gromacs/top/oplsaa.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
et 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_139 1 ETH C1 1 -0.189 12.01
2 opls_139 1 ETH C2 2 -0.155 12.01
3 opls_140 1 ETH H1 3 0.0059 1.008
4 opls_140 1 ETH H2 4 0.0059 1.008
5 opls_140 1 ETH H3 5 0.0059 1.008
6 opls_140 1 ETH H4 6 0.0056 1.008
7 opls_140 1 ETH H5 7 0.0056 1.008
8 opls_140 1 ETH H6 8 0.0056 1.008
[ bonds ]
; ai aj funct b0 kb
1 2 1
1 3 1
1 4 1
1 5 1
2 6 1
2 7 1
2 8 1
[ angles ]
; ai aj ak funct phi0 kphi
;around c1
3 1 4 1
4 1 5 1
3 1 5 1
2 1 3 1
2 1 4 1
2 1 5 1
;around c2
1 2 6 1
6 2 8 1
6 2 7 1
7 2 8 1
1 2 7 1
1 2 8 1
[ dihedrals ]
; ai aj ak al funct
3 1 2 6 3
3 1 2 7 3
3 1 2 8 3
4 1 2 6 3
4 1 2 7 3
4 1 2 8 3
5 1 2 6 3
5 1 2 7 3
5 1 2 8 3
[ System ]
; any text here
first one
[ molecules ]
;Name count
et 1' > et.top
Проверяем правильность выбора¶
In [18]:
%%bash
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
grompp -f be.mdp -c et.gro -p et.top -o et_test.tpr
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) 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 (-:
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 8 Mb of data
--2016-05-04 20:17:47-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1356 (1.3K)
Saving to: `be.mdp.2'
0K . 100% 140M=0s
2016-05-04 20:17:47 (140 MB/s) - `be.mdp.2' saved [1356/1356]
Option Filename Type Description
------------------------------------------------------------
-f be.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c et.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 et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o et_test.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 0 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.1#
NOTE 1 [file be.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file be.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 3 [file et.top, line 60]:
System has non-zero total charge: -0.309500
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.
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 4 [file be.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 4 notes
gcq#238: "Uh-oh" (Tinky Winky)
Скачаем 5 файлов с разными параметрами контроля температуры¶
In [19]:
%%bash
### метод Берендсена для контроля температуры.
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
### метод "Velocity rescale" для контроля температуры.
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
### метод Нуза-Хувера для контроля температуры.
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
### метод Андерсена для контроля температуры.
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
### метод стохастической молекулярной динамики.
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
--2016-05-04 20:21:15-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1356 (1.3K)
Saving to: `be.mdp.3'
0K . 100% 131M=0s
2016-05-04 20:21:15 (131 MB/s) - `be.mdp.3' saved [1356/1356]
--2016-05-04 20:21:15-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1427 (1.4K)
Saving to: `vr.mdp'
0K . 100% 167M=0s
2016-05-04 20:21:15 (167 MB/s) - `vr.mdp' saved [1427/1427]
--2016-05-04 20:21:15-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1429 (1.4K)
Saving to: `nh.mdp'
0K . 100% 150M=0s
2016-05-04 20:21:15 (150 MB/s) - `nh.mdp' saved [1429/1429]
--2016-05-04 20:21:15-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1426 (1.4K)
Saving to: `an.mdp'
0K . 100% 169M=0s
2016-05-04 20:21:15 (169 MB/s) - `an.mdp' saved [1426/1426]
--2016-05-04 20:21:15-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1441 (1.4K)
Saving to: `sd.mdp'
0K . 100% 173M=0s
2016-05-04 20:21:15 (173 MB/s) - `sd.mdp' saved [1441/1441]
Cтроим входные файлы для молекулярно-динамического движка mdrun с помощью grompp:¶
In [23]:
%%bash
# Зададим список i. По нему пустим grompp
for i in be nh vr an sd; do
grompp -f ${i}.mdp -c et.gro -p et.top -o et_${i}.tpr
done
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) 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 (-:
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 8 Mb of data
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) 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 (-:
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 8 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 (-:
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 8 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 (-:
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 8 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 (-:
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 8 Mb of data
Option Filename Type Description
------------------------------------------------------------
-f be.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c et.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 et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o et_be.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 0 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'
NOTE 1 [file be.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file be.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 3 [file et.top, line 60]:
System has non-zero total charge: -0.309500
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.
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 4 [file be.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 4 notes
gcq#252: "It's Coming Right For Us !" (South Park)
Option Filename Type Description
------------------------------------------------------------
-f nh.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c et.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 et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o et_nh.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 0 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.1#
NOTE 1 [file nh.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file nh.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 3 [file et.top, line 60]:
System has non-zero total charge: -0.309500
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.
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 4 [file nh.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 4 notes
gcq#1: "I Live the Life They Wish They Did" (Tricky)
Option Filename Type Description
------------------------------------------------------------
-f vr.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c et.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 et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o et_vr.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 0 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.2#
NOTE 1 [file vr.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 2 [file et.top, line 60]:
System has non-zero total charge: -0.309500
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.
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 3 [file vr.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 3 notes
gcq#1: "I Live the Life They Wish They Did" (Tricky)
Option Filename Type Description
------------------------------------------------------------
-f an.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c et.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 et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o et_an.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 0 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.3#
NOTE 1 [file an.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 2 [file et.top, line 60]:
System has non-zero total charge: -0.309500
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.
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 3 [file an.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 3 notes
gcq#1: "I Live the Life They Wish They Did" (Tricky)
Option Filename Type Description
------------------------------------------------------------
-f sd.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c et.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 et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o et_sd.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 0 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.4#
NOTE 1 [file sd.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Setting the LD random seed to 7147
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 2 [file et.top, line 60]:
System has non-zero total charge: -0.309500
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.
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 3 [file sd.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 3 notes
gcq#116: "If You're So Special Why aren't You Dead ?" (The Breeders)
Получили набор из 5 .tpr файлов для молеклярно-механического движка (по сути есть объединение gro, top и mdp).
Запускаем mdrun (молеклярно-механический движок)¶
In [24]:
%%bash
for i in be nh vr an sd; do
mdrun -deffnm et_${i} -v -nt 1
done
:-) G R O M A C S (-:
Getting the Right Output Means no Artefacts in Calculating Stuff
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_be.tpr Input Run input file: tpr tpb tpa
-o et_be.trr Output Full precision trajectory: trr trj cpt
-x et_be.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_be.cpt Input, Opt. Checkpoint file
-cpo et_be.cpt Output, Opt. Checkpoint file
-c et_be.gro Output Structure file: gro g96 pdb etc.
-e et_be.edr Output Energy file
-g et_be.log Output Log file
-dhdl et_be.xvg Output, Opt. xvgr/xmgr file
-field et_be.xvg Output, Opt. xvgr/xmgr file
-table et_be.xvg Input, Opt. xvgr/xmgr file
-tablep et_be.xvg Input, Opt. xvgr/xmgr file
-tableb et_be.xvg Input, Opt. xvgr/xmgr file
-rerun et_be.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_be.xvg Output, Opt. xvgr/xmgr file
-tpid et_be.xvg Output, Opt. xvgr/xmgr file
-ei et_be.edi Input, Opt. ED sampling input
-eo et_be.edo Output, Opt. ED sampling output
-j et_be.gct Input, Opt. General coupling stuff
-jo et_be.gct Output, Opt. General coupling stuff
-ffout et_be.xvg Output, Opt. xvgr/xmgr file
-devout et_be.xvg Output, Opt. xvgr/xmgr file
-runav et_be.xvg Output, Opt. xvgr/xmgr file
-px et_be.xvg Output, Opt. xvgr/xmgr file
-pf et_be.xvg Output, Opt. xvgr/xmgr file
-mtx et_be.mtx Output, Opt. Hessian matrix
-dn et_be.ndx Output, Opt. Index file
-multidir et_be 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 et_be 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 1 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 et_be.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.290 3.784 86.9
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 391.172 6565.376 0.004
gcq#317: "It's Unacceptable That Choclate Makes You Fat" (MI 3)
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_nh.tpr Input Run input file: tpr tpb tpa
-o et_nh.trr Output Full precision trajectory: trr trj cpt
-x et_nh.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_nh.cpt Input, Opt. Checkpoint file
-cpo et_nh.cpt Output, Opt. Checkpoint file
-c et_nh.gro Output Structure file: gro g96 pdb etc.
-e et_nh.edr Output Energy file
-g et_nh.log Output Log file
-dhdl et_nh.xvg Output, Opt. xvgr/xmgr file
-field et_nh.xvg Output, Opt. xvgr/xmgr file
-table et_nh.xvg Input, Opt. xvgr/xmgr file
-tablep et_nh.xvg Input, Opt. xvgr/xmgr file
-tableb et_nh.xvg Input, Opt. xvgr/xmgr file
-rerun et_nh.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_nh.xvg Output, Opt. xvgr/xmgr file
-tpid et_nh.xvg Output, Opt. xvgr/xmgr file
-ei et_nh.edi Input, Opt. ED sampling input
-eo et_nh.edo Output, Opt. ED sampling output
-j et_nh.gct Input, Opt. General coupling stuff
-jo et_nh.gct Output, Opt. General coupling stuff
-ffout et_nh.xvg Output, Opt. xvgr/xmgr file
-devout et_nh.xvg Output, Opt. xvgr/xmgr file
-runav et_nh.xvg Output, Opt. xvgr/xmgr file
-px et_nh.xvg Output, Opt. xvgr/xmgr file
-pf et_nh.xvg Output, Opt. xvgr/xmgr file
-mtx et_nh.mtx Output, Opt. Hessian matrix
-dn et_nh.ndx Output, Opt. Index file
-multidir et_nh 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 et_nh 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 1 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 et_nh.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.430 3.593 95.5
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 375.206 6297.402 0.004
gcq#45: "This May Come As a Shock" (F. Black)
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_vr.tpr Input Run input file: tpr tpb tpa
-o et_vr.trr Output Full precision trajectory: trr trj cpt
-x et_vr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_vr.cpt Input, Opt. Checkpoint file
-cpo et_vr.cpt Output, Opt. Checkpoint file
-c et_vr.gro Output Structure file: gro g96 pdb etc.
-e et_vr.edr Output Energy file
-g et_vr.log Output Log file
-dhdl et_vr.xvg Output, Opt. xvgr/xmgr file
-field et_vr.xvg Output, Opt. xvgr/xmgr file
-table et_vr.xvg Input, Opt. xvgr/xmgr file
-tablep et_vr.xvg Input, Opt. xvgr/xmgr file
-tableb et_vr.xvg Input, Opt. xvgr/xmgr file
-rerun et_vr.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_vr.xvg Output, Opt. xvgr/xmgr file
-tpid et_vr.xvg Output, Opt. xvgr/xmgr file
-ei et_vr.edi Input, Opt. ED sampling input
-eo et_vr.edo Output, Opt. ED sampling output
-j et_vr.gct Input, Opt. General coupling stuff
-jo et_vr.gct Output, Opt. General coupling stuff
-ffout et_vr.xvg Output, Opt. xvgr/xmgr file
-devout et_vr.xvg Output, Opt. xvgr/xmgr file
-runav et_vr.xvg Output, Opt. xvgr/xmgr file
-px et_vr.xvg Output, Opt. xvgr/xmgr file
-pf et_vr.xvg Output, Opt. xvgr/xmgr file
-mtx et_vr.mtx Output, Opt. Hessian matrix
-dn et_vr.ndx Output, Opt. Index file
-multidir et_vr 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 et_vr 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 1 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 et_vr.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.360 3.631 92.5
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 383.023 6428.598 0.004
gcq#139: "I Wrapped a Newspaper Round My Head" (F. Zappa)
:-) G R O M A C S (-:
Great Red Oystrich Makes All Chemists Sane
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_an.tpr Input Run input file: tpr tpb tpa
-o et_an.trr Output Full precision trajectory: trr trj cpt
-x et_an.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_an.cpt Input, Opt. Checkpoint file
-cpo et_an.cpt Output, Opt. Checkpoint file
-c et_an.gro Output Structure file: gro g96 pdb etc.
-e et_an.edr Output Energy file
-g et_an.log Output Log file
-dhdl et_an.xvg Output, Opt. xvgr/xmgr file
-field et_an.xvg Output, Opt. xvgr/xmgr file
-table et_an.xvg Input, Opt. xvgr/xmgr file
-tablep et_an.xvg Input, Opt. xvgr/xmgr file
-tableb et_an.xvg Input, Opt. xvgr/xmgr file
-rerun et_an.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_an.xvg Output, Opt. xvgr/xmgr file
-tpid et_an.xvg Output, Opt. xvgr/xmgr file
-ei et_an.edi Input, Opt. ED sampling input
-eo et_an.edo Output, Opt. ED sampling output
-j et_an.gct Input, Opt. General coupling stuff
-jo et_an.gct Output, Opt. General coupling stuff
-ffout et_an.xvg Output, Opt. xvgr/xmgr file
-devout et_an.xvg Output, Opt. xvgr/xmgr file
-runav et_an.xvg Output, Opt. xvgr/xmgr file
-px et_an.xvg Output, Opt. xvgr/xmgr file
-pf et_an.xvg Output, Opt. xvgr/xmgr file
-mtx et_an.mtx Output, Opt. Hessian matrix
-dn et_an.ndx Output, Opt. Index file
-multidir et_an 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 et_an 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 1 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 et_an.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.270 3.495 93.6
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 393.565 6605.531 0.004
gcq#117: "The Path Of the Righteous Man is Beset On All Sides With the Iniquities Of the Selfish and the Tyranny Of Evil Men." (Pulp Fiction)
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_sd.tpr Input Run input file: tpr tpb tpa
-o et_sd.trr Output Full precision trajectory: trr trj cpt
-x et_sd.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_sd.cpt Input, Opt. Checkpoint file
-cpo et_sd.cpt Output, Opt. Checkpoint file
-c et_sd.gro Output Structure file: gro g96 pdb etc.
-e et_sd.edr Output Energy file
-g et_sd.log Output Log file
-dhdl et_sd.xvg Output, Opt. xvgr/xmgr file
-field et_sd.xvg Output, Opt. xvgr/xmgr file
-table et_sd.xvg Input, Opt. xvgr/xmgr file
-tablep et_sd.xvg Input, Opt. xvgr/xmgr file
-tableb et_sd.xvg Input, Opt. xvgr/xmgr file
-rerun et_sd.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_sd.xvg Output, Opt. xvgr/xmgr file
-tpid et_sd.xvg Output, Opt. xvgr/xmgr file
-ei et_sd.edi Input, Opt. ED sampling input
-eo et_sd.edo Output, Opt. ED sampling output
-j et_sd.gct Input, Opt. General coupling stuff
-jo et_sd.gct Output, Opt. General coupling stuff
-ffout et_sd.xvg Output, Opt. xvgr/xmgr file
-devout et_sd.xvg Output, Opt. xvgr/xmgr file
-runav et_sd.xvg Output, Opt. xvgr/xmgr file
-px et_sd.xvg Output, Opt. xvgr/xmgr file
-pf et_sd.xvg Output, Opt. xvgr/xmgr file
-mtx et_sd.mtx Output, Opt. Hessian matrix
-dn et_sd.ndx Output, Opt. Index file
-multidir et_sd 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 et_sd 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 1 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 et_sd.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.910 4.111 95.1
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 345.002 5524.319 0.004
gcq#211: "They're Red Hot" (Red Hot Chili Peppers)
Визуальный анализ в PyMol¶
In [26]:
%%bash
for i in be nh vr an sd; do
trjconv -f et_${i}.trr -s et_${i}.tpr -o et_${i}.pdb
done
## В Putty: указывал номера групп.
Select group for output Select group for output Select group for output Select group for output 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f et_be.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o et_be.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s et_be.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 et_be.tpr, VERSION 4.5.5 (single precision)
Reading file et_be.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group:
-------------------------------------------------------
Program trjconv, 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
-------------------------------------------------------
"Your Proposal is Accepted" (Men In Black)
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f et_nh.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o et_nh.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s et_nh.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 et_nh.tpr, VERSION 4.5.5 (single precision)
Reading file et_nh.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group:
-------------------------------------------------------
Program trjconv, 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
-------------------------------------------------------
"Your Proposal is Accepted" (Men In Black)
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f et_vr.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o et_vr.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s et_vr.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 et_vr.tpr, VERSION 4.5.5 (single precision)
Reading file et_vr.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group:
-------------------------------------------------------
Program trjconv, 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
-------------------------------------------------------
"Your Proposal is Accepted" (Men In Black)
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f et_an.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o et_an.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s et_an.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 et_an.tpr, VERSION 4.5.5 (single precision)
Reading file et_an.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group:
-------------------------------------------------------
Program trjconv, 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
-------------------------------------------------------
"Your Proposal is Accepted" (Men In Black)
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f et_sd.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o et_sd.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s et_sd.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 et_sd.tpr, VERSION 4.5.5 (single precision)
Reading file et_sd.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group:
-------------------------------------------------------
Program trjconv, 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
-------------------------------------------------------
"Your Proposal is Accepted" (Men In Black)
In [27]:
import __main__
__main__.pymol_argv = [ 'pymol', '-cp' ]
import pymol
pymol.finish_launching()
from pymol import cmd
In [106]:
cmd.do('''
reinitialize
set ray_trace_mode, 0; red
set ray_opaque_background, off
set antialias, .5
set light_count, 8
set ambient, 0.5
set ray_trace_color, red
set cartoon_side_chain_helper, on
cd /home/students/y12/iltarn/Term6/Practice5
load et_sd.pdb, sd
color green, sd
translate [-10,0,0], object=sd
load et_an.pdb, an
color firebrick, an
translate [-5,0,0], object=an
load et_vr.pdb, vr
color orange, vr
load et_nh.pdb, nh
color blue, nh
translate [5,0,0], object=nh
load et_be.pdb, be
color gray, be
translate [10,0,0], object=be
center all
zoom all, -10
set all_states, on
ray 1200,150
png pic1.png
''')
In [107]:
Image(filename='pic1.png')
Out[107]:
In [108]:
cmd.do('''
rotate x, 45
ray 1200,150
png pic1_45.png
''')
In [110]:
Image(filename='pic1_45.png')
Out[110]:
Сравним потенциальную энергию связи и кинетическую энергию для каждой из 5 систем.¶
In [114]:
%%bash
for i in be nh vr an sd; do
g_energy -f et_${i}.edr -o et_${i}_en.xvg -xvg none
done
# Делал через консоль в Putty, вбивая 8&9.
In [115]:
%%bash
set datafile commentschars "#@&"
plot "./et_be_en.xvg" using 1:2, "./et_be_en.xvg" using 1:3
plot "./et_sd_en.xvg" using 1:2, "./et_sd_en.xvg" using 1:3
In [116]:
%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
1) Метод стохастической молекулярной динамики¶
In [128]:
a = np.loadtxt("/home/students/y12/iltarn/Term6/Practice5/et_sd_en.xvg")
x_o=a[:,0]
y_o=a[:,1]
z_o=a[:,2]
#Plot it
plt.plot(x_o, y_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.show()
plt.plot(x_o, z_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.show()
2) Метод "Velocity rescale"¶
In [129]:
a = np.loadtxt("/home/students/y12/iltarn/Term6/Practice5/et_vr_en.xvg")
x_o=a[:,0]
y_o=a[:,1]
z_o=a[:,2]
#Plot it
plt.plot(x_o, y_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.show()
plt.plot(x_o, z_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.show()
3) Метод Берендсена¶
In [130]:
a = np.loadtxt("/home/students/y12/iltarn/Term6/Practice5/et_be_en.xvg")
x_o=a[:,0]
y_o=a[:,1]
z_o=a[:,2]
#Plot it
plt.plot(x_o, y_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.show()
plt.plot(x_o, z_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.show()
4) Метод Нуза-Хувера¶
In [131]:
a = np.loadtxt("/home/students/y12/iltarn/Term6/Practice5/et_nh_en.xvg")
x_o=a[:,0]
y_o=a[:,1]
z_o=a[:,2]
#Plot it
plt.plot(x_o, y_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.show()
plt.plot(x_o, z_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.show()
5) Метод Андерсена¶
In [132]:
a = np.loadtxt("/home/students/y12/iltarn/Term6/Practice5/et_an_en.xvg")
x_o=a[:,0]
y_o=a[:,1]
z_o=a[:,2]
#Plot it
plt.plot(x_o, y_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.show()
plt.plot(x_o, z_o, "ro")
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.show()
Распределение длины связи С-С за время моделирования¶
In [133]:
%%bash
# сделаем индекс-файл с одной связью
echo '[ b ]
1 2 ' > b.ndx
In [1]:
%%bash
# запустим утилиту по анализу связей g_bond:
for i in be vr nh an sd; do
g_bond -f et_${i}.trr -s et_${i}.tpr -o bond_${i}.xvg -n b.ndx -xvg none
done
Total number of samples : 251 Mean : 0.152816 Standard deviation of the distribution: 0.00198159 Standard deviation of the mean : 0.000125077 Total number of samples : 251 Mean : 0.152947 Standard deviation of the distribution: 0.00363286 Standard deviation of the mean : 0.000229304 Total number of samples : 251 Mean : 0.152841 Standard deviation of the distribution: 0.00301553 Standard deviation of the mean : 0.000190338 Total number of samples : 251 Mean : 0.152883 Standard deviation of the distribution: 0.00132163 Standard deviation of the mean : 8.34206e-05 Total number of samples : 251 Mean : 0.152719 Standard deviation of the distribution: 0.00371478 Standard deviation of the mean : 0.000234475
:-) 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.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f et_be.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s et_be.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_be.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.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 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 200 time 200.000
gcq#93: "Pretend That You're Hercule Poirot" (TeX)
:-) 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.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f et_vr.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s et_vr.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_vr.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.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 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.1#
Reading frame 200 time 200.000
gcq#93: "Pretend That You're Hercule Poirot" (TeX)
:-) 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.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f et_nh.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s et_nh.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_nh.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.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 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.2#
Reading frame 200 time 200.000
gcq#93: "Pretend That You're Hercule Poirot" (TeX)
:-) 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.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f et_an.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s et_an.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_an.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.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 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.3#
Reading frame 200 time 200.000
gcq#93: "Pretend That You're Hercule Poirot" (TeX)
:-) 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.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f et_sd.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s et_sd.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_sd.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.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 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.4#
Reading frame 200 time 200.000
gcq#93: "Pretend That You're Hercule Poirot" (TeX)
1) Метод стохастической молекулярной динамики¶
In [7]:
%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
# Использовал следующий скрипт:
#a = np.loadtxt("distance.xvg")
#plt.figure(figsize=(10,10))
#plt.subplot(211)
#x=a[:,1]
#n, bins, patches = plt.hist(x, 50, facecolor='m', alpha=0.75)
#plt.xlabel('Distance')
#plt.subplot(212)
#x=a[:,0]
#y=a[:,1]
#plt.scatter(x, y)
#plt.xlabel('time, ps')
#plt.ylabel('dist')
#plt.savefig('plot_be.png')
#plt.show()
Image(filename='plot_sd.png')
Out[7]:
2) Метод "Velocity rescale"¶
In [6]:
Image(filename='plot_vr.png')
Out[6]:
3) Метод Берендсена¶
In [5]:
Image(filename='plot_be.png')
Out[5]:
4) Метод Нуза-Хувера¶
In [4]:
Image(filename='plot_nh.png')
Out[4]:
5) Метод Андерсена¶
In [3]:
Image(filename='plot_an.png')
Out[3]:
Зависмость быстродействия от алгоритма¶
In [16]:
%%bash
# добавил подсчет времени и перезапустил mdrun
rm times
for i in be vr nh an sd; do
start=$(date +%s.%N)
mdrun -deffnm et_${i} -v -nt 1
dur=$(echo "$(date +%s.%N) - $start" | bc)
echo ${i} $dur >> times
done
cat times
be 3.620534748 vr 4.001735273 nh 4.033838250 an 3.484786826 sd 4.630439716
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_be.tpr Input Run input file: tpr tpb tpa
-o et_be.trr Output Full precision trajectory: trr trj cpt
-x et_be.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_be.cpt Input, Opt. Checkpoint file
-cpo et_be.cpt Output, Opt. Checkpoint file
-c et_be.gro Output Structure file: gro g96 pdb etc.
-e et_be.edr Output Energy file
-g et_be.log Output Log file
-dhdl et_be.xvg Output, Opt. xvgr/xmgr file
-field et_be.xvg Output, Opt. xvgr/xmgr file
-table et_be.xvg Input, Opt. xvgr/xmgr file
-tablep et_be.xvg Input, Opt. xvgr/xmgr file
-tableb et_be.xvg Input, Opt. xvgr/xmgr file
-rerun et_be.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_be.xvg Output, Opt. xvgr/xmgr file
-tpid et_be.xvg Output, Opt. xvgr/xmgr file
-ei et_be.edi Input, Opt. ED sampling input
-eo et_be.edo Output, Opt. ED sampling output
-j et_be.gct Input, Opt. General coupling stuff
-jo et_be.gct Output, Opt. General coupling stuff
-ffout et_be.xvg Output, Opt. xvgr/xmgr file
-devout et_be.xvg Output, Opt. xvgr/xmgr file
-runav et_be.xvg Output, Opt. xvgr/xmgr file
-px et_be.xvg Output, Opt. xvgr/xmgr file
-pf et_be.xvg Output, Opt. xvgr/xmgr file
-mtx et_be.mtx Output, Opt. Hessian matrix
-dn et_be.ndx Output, Opt. Index file
-multidir et_be 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 et_be 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 1 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
Back Off! I just backed up et_be.log to ./#et_be.log.3#
Getting Loaded...
Reading file et_be.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_be.trr to ./#et_be.trr.3#
Back Off! I just backed up et_be.edr to ./#et_be.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_be.gro to ./#et_be.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.380 3.611 93.6
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 380.757 6390.559 0.004
gcq#91: "I Can't Shake It" (Dinosaur Jr)
:-) 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.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s et_vr.tpr Input Run input file: tpr tpb tpa
-o et_vr.trr Output Full precision trajectory: trr trj cpt
-x et_vr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_vr.cpt Input, Opt. Checkpoint file
-cpo et_vr.cpt Output, Opt. Checkpoint file
-c et_vr.gro Output Structure file: gro g96 pdb etc.
-e et_vr.edr Output Energy file
-g et_vr.log Output Log file
-dhdl et_vr.xvg Output, Opt. xvgr/xmgr file
-field et_vr.xvg Output, Opt. xvgr/xmgr file
-table et_vr.xvg Input, Opt. xvgr/xmgr file
-tablep et_vr.xvg Input, Opt. xvgr/xmgr file
-tableb et_vr.xvg Input, Opt. xvgr/xmgr file
-rerun et_vr.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_vr.xvg Output, Opt. xvgr/xmgr file
-tpid et_vr.xvg Output, Opt. xvgr/xmgr file
-ei et_vr.edi Input, Opt. ED sampling input
-eo et_vr.edo Output, Opt. ED sampling output
-j et_vr.gct Input, Opt. General coupling stuff
-jo et_vr.gct Output, Opt. General coupling stuff
-ffout et_vr.xvg Output, Opt. xvgr/xmgr file
-devout et_vr.xvg Output, Opt. xvgr/xmgr file
-runav et_vr.xvg Output, Opt. xvgr/xmgr file
-px et_vr.xvg Output, Opt. xvgr/xmgr file
-pf et_vr.xvg Output, Opt. xvgr/xmgr file
-mtx et_vr.mtx Output, Opt. Hessian matrix
-dn et_vr.ndx Output, Opt. Index file
-multidir et_vr 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 et_vr 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 1 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
Back Off! I just backed up et_vr.log to ./#et_vr.log.3#
Getting Loaded...
Reading file et_vr.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_vr.trr to ./#et_vr.trr.3#
Back Off! I just backed up et_vr.edr to ./#et_vr.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_vr.gro to ./#et_vr.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.730 3.991 93.5
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 345.029 5790.908 0.004
gcq#185: "It is Lunchtime" (A.R. Van Buuren)
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_nh.tpr Input Run input file: tpr tpb tpa
-o et_nh.trr Output Full precision trajectory: trr trj cpt
-x et_nh.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_nh.cpt Input, Opt. Checkpoint file
-cpo et_nh.cpt Output, Opt. Checkpoint file
-c et_nh.gro Output Structure file: gro g96 pdb etc.
-e et_nh.edr Output Energy file
-g et_nh.log Output Log file
-dhdl et_nh.xvg Output, Opt. xvgr/xmgr file
-field et_nh.xvg Output, Opt. xvgr/xmgr file
-table et_nh.xvg Input, Opt. xvgr/xmgr file
-tablep et_nh.xvg Input, Opt. xvgr/xmgr file
-tableb et_nh.xvg Input, Opt. xvgr/xmgr file
-rerun et_nh.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_nh.xvg Output, Opt. xvgr/xmgr file
-tpid et_nh.xvg Output, Opt. xvgr/xmgr file
-ei et_nh.edi Input, Opt. ED sampling input
-eo et_nh.edo Output, Opt. ED sampling output
-j et_nh.gct Input, Opt. General coupling stuff
-jo et_nh.gct Output, Opt. General coupling stuff
-ffout et_nh.xvg Output, Opt. xvgr/xmgr file
-devout et_nh.xvg Output, Opt. xvgr/xmgr file
-runav et_nh.xvg Output, Opt. xvgr/xmgr file
-px et_nh.xvg Output, Opt. xvgr/xmgr file
-pf et_nh.xvg Output, Opt. xvgr/xmgr file
-mtx et_nh.mtx Output, Opt. Hessian matrix
-dn et_nh.ndx Output, Opt. Index file
-multidir et_nh 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 et_nh 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 1 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
Back Off! I just backed up et_nh.log to ./#et_nh.log.3#
Getting Loaded...
Reading file et_nh.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_nh.trr to ./#et_nh.trr.3#
Back Off! I just backed up et_nh.edr to ./#et_nh.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_nh.gro to ./#et_nh.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.740 4.024 92.9
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 344.106 5775.425 0.004
gcq#279: "I Feel a Great Disturbance in the Force" (The Emperor Strikes Back)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_an.tpr Input Run input file: tpr tpb tpa
-o et_an.trr Output Full precision trajectory: trr trj cpt
-x et_an.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_an.cpt Input, Opt. Checkpoint file
-cpo et_an.cpt Output, Opt. Checkpoint file
-c et_an.gro Output Structure file: gro g96 pdb etc.
-e et_an.edr Output Energy file
-g et_an.log Output Log file
-dhdl et_an.xvg Output, Opt. xvgr/xmgr file
-field et_an.xvg Output, Opt. xvgr/xmgr file
-table et_an.xvg Input, Opt. xvgr/xmgr file
-tablep et_an.xvg Input, Opt. xvgr/xmgr file
-tableb et_an.xvg Input, Opt. xvgr/xmgr file
-rerun et_an.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_an.xvg Output, Opt. xvgr/xmgr file
-tpid et_an.xvg Output, Opt. xvgr/xmgr file
-ei et_an.edi Input, Opt. ED sampling input
-eo et_an.edo Output, Opt. ED sampling output
-j et_an.gct Input, Opt. General coupling stuff
-jo et_an.gct Output, Opt. General coupling stuff
-ffout et_an.xvg Output, Opt. xvgr/xmgr file
-devout et_an.xvg Output, Opt. xvgr/xmgr file
-runav et_an.xvg Output, Opt. xvgr/xmgr file
-px et_an.xvg Output, Opt. xvgr/xmgr file
-pf et_an.xvg Output, Opt. xvgr/xmgr file
-mtx et_an.mtx Output, Opt. Hessian matrix
-dn et_an.ndx Output, Opt. Index file
-multidir et_an 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 et_an 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 1 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
Back Off! I just backed up et_an.log to ./#et_an.log.3#
Getting Loaded...
Reading file et_an.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_an.trr to ./#et_an.trr.3#
Back Off! I just backed up et_an.edr to ./#et_an.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_an.gro to ./#et_an.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.260 3.475 93.8
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 394.772 6625.794 0.004
gcq#258: "In the End Science Comes Down to Praying" (P. v.d. Berg)
:-) 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 (-:
Option Filename Type Description
------------------------------------------------------------
-s et_sd.tpr Input Run input file: tpr tpb tpa
-o et_sd.trr Output Full precision trajectory: trr trj cpt
-x et_sd.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_sd.cpt Input, Opt. Checkpoint file
-cpo et_sd.cpt Output, Opt. Checkpoint file
-c et_sd.gro Output Structure file: gro g96 pdb etc.
-e et_sd.edr Output Energy file
-g et_sd.log Output Log file
-dhdl et_sd.xvg Output, Opt. xvgr/xmgr file
-field et_sd.xvg Output, Opt. xvgr/xmgr file
-table et_sd.xvg Input, Opt. xvgr/xmgr file
-tablep et_sd.xvg Input, Opt. xvgr/xmgr file
-tableb et_sd.xvg Input, Opt. xvgr/xmgr file
-rerun et_sd.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_sd.xvg Output, Opt. xvgr/xmgr file
-tpid et_sd.xvg Output, Opt. xvgr/xmgr file
-ei et_sd.edi Input, Opt. ED sampling input
-eo et_sd.edo Output, Opt. ED sampling output
-j et_sd.gct Input, Opt. General coupling stuff
-jo et_sd.gct Output, Opt. General coupling stuff
-ffout et_sd.xvg Output, Opt. xvgr/xmgr file
-devout et_sd.xvg Output, Opt. xvgr/xmgr file
-runav et_sd.xvg Output, Opt. xvgr/xmgr file
-px et_sd.xvg Output, Opt. xvgr/xmgr file
-pf et_sd.xvg Output, Opt. xvgr/xmgr file
-mtx et_sd.mtx Output, Opt. Hessian matrix
-dn et_sd.ndx Output, Opt. Index file
-multidir et_sd 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 et_sd 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 1 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
Back Off! I just backed up et_sd.log to ./#et_sd.log.3#
Getting Loaded...
Reading file et_sd.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_sd.trr to ./#et_sd.trr.3#
Back Off! I just backed up et_sd.edr to ./#et_sd.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_sd.gro to ./#et_sd.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 4.340 4.621 93.9
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 310.820 4976.979 0.005
gcq#101: "My Heart is Just a Muscle In a Cavity" (F. Black)
Выводы¶
Метод стохастической молекулярной динамики: длина связи меняется по синусоиде, что интересно. Работает дольше всех.
Метод "Velocity rescale": колебание длины связи затухает со временем, распределение длин связей напоминает распределение Больцмана. Здесь температура системы остается постоянной за счет пересчета скоростей молекул на каждом шаге.
Метод Берендсена: распределение длин связей напоминает распределение Больцмана. Колебания энергий затухают экспоненциально. Пересчет скоростей реже, чем в предыдущем методе, поэтому допускаются колебания температуры.
Метод Нуза-Хувера: распределение больше прочих похоже на распределение Больцмана, свобода колебаний длины связи примерно такая же, как и у предыдущего метода. Имеет самые высокоэнергетические выбросы (и по потенциальной, и по кинетической энергиям). Метод едва ли пригоден для анализа небольших молекул, так как дает сравнительно огромные "выбросы" по значениям энергии.
Метод Андерсена: правая часть распределения длин связей напоминает распределение Больцмана, колебание длины связи зажато в узком коридоре. Работает быстрее всех. По энергиям отстает от других методов. Ансамбль канонический: температура системы остается постоянной за счет обмена энергией с термостатом. Так как метод предполагает наличие столкновений молекул, то он не подходит для одиночных молекул, так как им не с чем сталкиваться.
Основываясь на всем, что приведено и сказано выше, для решения данной задачи, как кажется, лучше подходят такие методы, как метод стохастической молекулярной динамики, метод Берендсена и метод Velocity rescale. Первый кажется более универсальным для низкомолекулярных соединений или небольшого их количества, так как допускает большое число степеней свободы, что, однако, приводит к более длительному времени работы.