Изучение работы методов контроля температуры в GROMACS¶
Цель: изучить, как реализован контроль температуры в молекулярной динамике на примере GROMACS. Объект исследования это одна молекула этана.
В консоли:
In []:
%%bash
make_ndx -f box_38.gro -o 1.ndx #r1, q - выбрали 1 остаток, добавилась 1 группа
editconf -f box_38.gro -o et1.gro -n 1.ndx
#зададим ячейку и расположим молекулу по центру ячейку
editconf -f et1.gro -o et.gro -d 2 -c
Построим файл топологии et.top для этана, подобрав типы атомов (согласно /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp):
In [6]:
ethane = """#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"""
with open('et.top', 'w') as w:
w.write(ethane)
Далее будем работать с 5 методами контроля температурой (даны соответствующие файлы):
be.mdp - метод Берендсена для контроля температуры,
vr.mdp - метод "Velocity rescale" для контроля температуры,
nh.mdp - метод Нуза-Хувера для контроля температуры,
an.mdp - метод Андерсена для контроля температуры,
sd.mdp - метод стохастической молекулярной динамики
Построим входные файлы для молекулярно-динамического движка mdrun с помощью grompp, на основне et.top с помощью grompp:
grompp -f be.mdp -c et.gro -p et.top -o et_be.tpr
In [7]:
%%bash
for i in $(echo be vr nh an sd); do
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/${i}.mdp
grompp -f $i.mdp -c et.gro -p et.top -o et_$i.tpr
mdrun -deffnm et_$i -v -nt 1;
done
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
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 ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
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 (-:
Gravel Rubs Often Many Awfully Cauterized Sores
:-) 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 (-:
Great Red Owns Many ACres of Sand
:-) 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
--2016-05-14 13:56:59-- 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.5'
0K . 100% 102M=0s
2016-05-14 13:56:59 (102 MB/s) - `be.mdp.5' 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_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'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41#
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#167: "Welcome to the Power Age" (2 Unlimited)
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
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
Back Off! I just backed up et_be.log to ./#et_be.log.9#
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: 3.320 3.510 94.6
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 387.638 6506.051 0.004
gcq#146: "A Protein is a Set Of Coordinates" (A.P. Heiner)
--2016-05-14 13:57:03-- 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.5'
0K . 100% 179M=0s
2016-05-14 13:57:03 (179 MB/s) - `vr.mdp.5' saved [1427/1427]
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.42#
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#261: "Live for Liposuction" (Robbie Williams)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
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
Back Off! I just backed up et_vr.log to ./#et_vr.log.9#
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: 3.380 3.609 93.7
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 380.757 6390.559 0.004
gcq#240: "Uh-oh, We're In Trouble" (Shampoo)
--2016-05-14 13:57:07-- 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.5'
0K . 100% 136M=0s
2016-05-14 13:57:07 (136 MB/s) - `nh.mdp.5' saved [1429/1429]
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.43#
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#355: "I Like You. I Will Kill You Last" (Tyler in Fishtank)
:-) 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_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
Back Off! I just backed up et_nh.log to ./#et_nh.log.9#
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: 3.390 3.576 94.8
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 379.633 6371.707 0.004
gcq#334: "Aber wenn der Quarterback kommt, um dir die Brille abzunehmen Sag ihm: Danke die bleibt wo sie ist" (Wir sind Helden)
--2016-05-14 13:57:11-- 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.5'
0K . 100% 177M=0s
2016-05-14 13:57:11 (177 MB/s) - `an.mdp.5' saved [1426/1426]
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.44#
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#334: "Aber wenn der Quarterback kommt, um dir die Brille abzunehmen Sag ihm: Danke die bleibt wo sie ist" (Wir sind Helden)
:-) G R O M A C S (-:
Gravel Rubs Often Many Awfully Cauterized Sores
:-) 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
Back Off! I just backed up et_an.log to ./#et_an.log.9#
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 3.436 95.2
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 393.565 6605.531 0.004
gcq#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
--2016-05-14 13:57:15-- 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.5'
0K . 100% 167M=0s
2016-05-14 13:57:15 (167 MB/s) - `sd.mdp.5' saved [1441/1441]
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.45#
NOTE 1 [file sd.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Setting the LD random seed to 29850
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#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) 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
Back Off! I just backed up et_sd.log to ./#et_sd.log.9#
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: 3.890 4.129 94.2
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 346.776 5552.722 0.004
gcq#156: "Rub It Right Accross Your Eyes" (F. Zappa)
In [15]:
%%bash
for i in $(echo be vr nh an sd); do
echo "2" | trjconv -f et_${i}.trr -s et_${i}.tpr -o et_${i}.pdb
done
Select group for output Selected 2: 'ETH' Select group for output Selected 2: 'ETH' Select group for output Selected 2: 'ETH' Select group for output Selected 2: 'ETH' Select group for output Selected 2: 'ETH'
:-) 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.
:-) 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: trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up et_be.pdb to ./#et_be.pdb.2#
-> frame 250 time 250.000
gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)
:-) 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.
:-) 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: trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up et_vr.pdb to ./#et_vr.pdb.2#
-> frame 250 time 250.000
gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)
:-) 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.
:-) 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: trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up et_nh.pdb to ./#et_nh.pdb.2#
-> frame 250 time 250.000
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.
:-) 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: trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up et_an.pdb to ./#et_an.pdb.2#
-> frame 250 time 250.000
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.
:-) 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: trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up et_sd.pdb to ./#et_sd.pdb.2#
-> frame 250 time 250.000
gcq#91: "I Can't Shake It" (Dinosaur Jr)
В полученных pdb-файлах можно рассмотреть изменения молекул (их длин связи и углов) со временем (с разными t). С разными параметрами контроля температуры изменения различны.
Сравним потенциальную энергию связи и кинетическую энергию для каждой из 5 систем.
Вытащим данные о времени и энергии для каждой системы.
Следующий шаг провели в консоли, вытаскивая данные о потенциальной энергии(8), кинетической (9) и общей энергией (10).
In []:
%%bash
for i in $(echo be vr nh an sd); do
g_energy -f et_${i}.edr -o et_${i}_en.xvg -xvg none
done
In []:
# а именно, в консоли были выполнены следующие команды:
g_energy -f et_an.edr -o et_an_en.xvg -xvg none
g_energy -f et_be.edr -o et_be_en.xvg -xvg none
g_energy -f et_nh.edr -o et_nh_en.xvg -xvg none
g_energy -f et_sd.edr -o et_sd_en.xvg -xvg none
g_energy -f et_vr.edr -o et_vr_en.xvg -xvg none
#с выбором 8, 9, 10
Построим графики изменения энергий.
In [4]:
%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
Сначала графики потенциальной энергии от времени.
In [33]:
a = np.loadtxt("et_an_en.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.title('Potential(time), an')
plt.show()
In [34]:
a = np.loadtxt("et_be_en.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.title('Potential(time), be')
plt.show()
In [35]:
a = np.loadtxt("et_nh_en.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.title('Potential(time), nh')
plt.show()
In [36]:
a = np.loadtxt("et_sd_en.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.title('Potential(time), sd')
plt.show()
In [37]:
a = np.loadtxt("et_vr_en.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Potential, kJ/mol')
plt.title('Potential(time), vr')
plt.show()
Теперь графики зависимости кинетической энергии от времени.
In [39]:
a = np.loadtxt("et_an_en.xvg")
x=a[:,0]
y=a[:,2]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.title('Kinetic(time), an')
plt.show()
In [40]:
a = np.loadtxt("et_be_en.xvg")
x=a[:,0]
y=a[:,2]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.title('Kinetic(time), be')
plt.show()
In [41]:
a = np.loadtxt("et_nh_en.xvg")
x=a[:,0]
y=a[:,2]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.title('Kinetic(time), nh')
plt.show()
In [42]:
a = np.loadtxt("et_sd_en.xvg")
x=a[:,0]
y=a[:,2]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.title('Kinetic(time), sd')
plt.show()
In [43]:
a = np.loadtxt("et_vr_en.xvg")
x=a[:,0]
y=a[:,2]
plt.scatter(x,y)
plt.xlabel('time, ps')
plt.ylabel('Kinetic, kJ/mol')
plt.title('Kinetic(time), vr')
plt.show()
Как видно из графиков, изменение энергии в различных методах происходит по-разному, при этом для изменений каждого метода можно выделить свои характерные особенности. Кроме того, интересно, что изменения потенциальной и кинетической энергии для одной системы происходит сходным образом.
Теперь рассмотрим распределение длинны связи С-С за время моделирования. Сначала создадим индекс файл с одной связью. В текстовом редакторе создайте файл b.ndx со следующим содержимым:
In [45]:
%%bash
echo -e "[ b ]\n1 2" > b.ndx
cat b.ndx
[ b ] 1 2
Запустим утилиту по анализу связей g_bond:
In [2]:
%%bash
for i in $(echo be vr nh an sd); do
g_bond -f et_${i}.trr -s et_${i}.tpr -o bond_${i}.xvg -d distance_$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 : 0.153293 Standard deviation of the distribution: 0.00353111 Standard deviation of the mean : 0.000222882
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) 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_be.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_be.xvg to ./#distance_be.xvg.1#
Reading frame 200 time 200.000
Back Off! I just backed up bond_be.xvg to ./#bond_be.xvg.2#
gcq#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) 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_vr.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_vr.xvg to ./#distance_vr.xvg.1#
Reading frame 200 time 200.000
Back Off! I just backed up bond_vr.xvg to ./#bond_vr.xvg.2#
gcq#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) 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_nh.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_nh.xvg to ./#distance_nh.xvg.1#
Reading frame 200 time 200.000
Back Off! I just backed up bond_nh.xvg to ./#bond_nh.xvg.2#
gcq#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) 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_an.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_an.xvg to ./#distance_an.xvg.1#
Reading frame 200 time 200.000
Back Off! I just backed up bond_an.xvg to ./#bond_an.xvg.2#
gcq#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) 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_sd.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_sd.xvg to ./#distance_sd.xvg.1#
Reading frame 200 time 200.000
Back Off! I just backed up bond_sd.xvg to ./#bond_sd.xvg.2#
gcq#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
Построим графики распределения длинн связей.
In [17]:
a = np.loadtxt("distance_an.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x, y)
plt.xlabel('time, ps')
plt.ylabel('distance, nm')
plt.title('Distance, an')
plt.show()
In [18]:
a = np.loadtxt("distance_be.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x, y)
plt.xlabel('time, ps')
plt.ylabel('distance, nm')
plt.title('Distance, be')
plt.show()
In [19]:
a = np.loadtxt("distance_nh.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x, y)
plt.xlabel('time, ps')
plt.ylabel('distance, nm')
plt.title('Distance, nh')
plt.show()
In [21]:
a = np.loadtxt("distance_sd.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x, y)
plt.xlabel('time, ps')
plt.ylabel('distance, nm')
plt.title('Distance, sd')
plt.show()
In [22]:
a = np.loadtxt("distance_vr.xvg")
x=a[:,0]
y=a[:,1]
plt.scatter(x, y)
plt.xlabel('time, ps')
plt.ylabel('distance, nm')
plt.title('Distance, vr')
plt.show()
