Изучение работы методов контроля температуры в молекулярной динамике

Цель: изучить, как реализован контроль температуры в молекулярной динамике на примере GROMACS.

Объект исследования это одна молекула этана.

Сначало был подготовлен файл координат и файл топологии этана.

In [5]:
%%bash
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro
#Был скачен gro файл с координатами этана.
#В ручную был построен файл топологии et.top для этана.

--2017-05-25 15:26:35--  http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.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: 399
Saving to: `etane.gro.2'

     0K                                                       100% 44.7M=0s

2017-05-25 15:26:35 (44.7 MB/s) - `etane.gro.2' saved [399/399]
In [31]:
%%bash
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
#5 файлов с разными параметрами контроля температуры

--2017-05-25 16:15:41--  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'

     0K .                                                     100%  118M=0s

2017-05-25 16:15:41 (118 MB/s) - `be.mdp' saved [1356/1356]

--2017-05-25 16:15:41--  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%  174M=0s

2017-05-25 16:15:41 (174 MB/s) - `vr.mdp' saved [1427/1427]

--2017-05-25 16:15:41--  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%  135M=0s

2017-05-25 16:15:41 (135 MB/s) - `nh.mdp' saved [1429/1429]

--2017-05-25 16:15:41--  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%  153M=0s

2017-05-25 16:15:41 (153 MB/s) - `an.mdp' saved [1426/1426]

--2017-05-25 16:15:41--  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%  149M=0s

2017-05-25 16:15:41 (149 MB/s) - `sd.mdp' saved [1441/1441]
In [38]:
#grompp -f be.mdp -c et.gro -p et.top -o et_be.tpr
#mdrun -deffnm et_be.tpr -v -nt 1
#echo 0|trjconv -f et_be.trr -s et_be.tpr -o et_be.pdb
#
import subprocess
names=['be', 'vr', 'nh', 'an', 'sd']

for i in names:
    cmd = 'grompp -f %s.mdp -c et.gro -p et.top -o et_%s.tpr >& log.grompp'  %(i,i)
    #print cmd
    subprocess.call(cmd, shell=True)
    cmd1 = 'mdrun -deffnm et_%s.tpr -v -nt 1'  %(i)
    #print cmd1
    subprocess.call(cmd1, shell=True)
    cmd2 = 'echo 0|trjconv -f et_%s.trr -s et_%s.tpr -o et_%s.pdb >& log.trjconv' %(i,i,i)
    #print cmd2
    subprocess.call(cmd2, shell=True)

Оценим тепловые колебания каждого метода:
be - метод Берендсена для контроля температуры - происходит вращение вокруг С-С связи
vr - метод "Velocity rescale" для контроля температуры - происходит вращение вокруг С-С связи и вокруг центра масс 
nh.mdp - метод Нуза-Хувера для контроля температуры - С-С связь стоит на месте, вращаются только водороды
an.mdp - метод Андерсена для контроля температуры - Молекула стоит на месте
sd.mdp - метод стохастической молекулярной динамики - Вращение произвольное и хаотичное

Сравним потенциальную энергию и кинетическую энергию для каждой из 5 систем.

In [41]:
for i in names:
    cmd = 'echo 10 | g_energy -f et_%s.tpr.edr -o 1et_%s_pot_en.xvg -xvg none' %(i,i)
    subprocess.call(cmd, shell=True)
    cmd = 'echo 11 | g_energy -f et_%s.tpr.edr -o 1et_%s_kin_en.xvg -xvg none' %(i,i)
    subprocess.call(cmd, shell=True)
In [ ]:
%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
from scipy import optimize 
import matplotlib.patches as mpatches
In [58]:
for filename in ['be']:#,'vr','nh','an','sd']:
    a= np.loadtxt('1et_%s_pot_en.xvg' % filename)
    b= np.loadtxt('1et_%s_kin_en.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    
    t2=b[:,0]
    y2=b[:,1]
    plt.plot()
    plt.plot(t1, y1, "b-", t2, y2, "r-" )
    red_patch = mpatches.Patch(color='red', label='Kinetic')
    blue_patch = mpatches.Patch(color='blue', label='Potential')
    plt.legend(handles=[red_patch,blue_patch])
    plt.title('Energies of %s system' % filename)
In [59]:
for filename in ['vr']:
    a= np.loadtxt('1et_%s_pot_en.xvg' % filename)
    b= np.loadtxt('1et_%s_kin_en.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    
    t2=b[:,0]
    y2=b[:,1]
    plt.plot()
    plt.plot(t1, y1, "b-", t2, y2, "r-" )
    red_patch = mpatches.Patch(color='red', label='Kinetic')
    blue_patch = mpatches.Patch(color='blue', label='Potential')
    plt.legend(handles=[red_patch,blue_patch])
    plt.title('Energies of %s system' % filename)
In [60]:
for filename in ['nh']:
    a= np.loadtxt('1et_%s_pot_en.xvg' % filename)
    b= np.loadtxt('1et_%s_kin_en.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    
    t2=b[:,0]
    y2=b[:,1]
    plt.plot()
    plt.plot(t1, y1, "b-", t2, y2, "r-" )
    red_patch = mpatches.Patch(color='red', label='Kinetic')
    blue_patch = mpatches.Patch(color='blue', label='Potential')
    plt.legend(handles=[red_patch,blue_patch])
    plt.title('Energies of %s system' % filename)
In [62]:
for filename in ['an']:
    a= np.loadtxt('1et_%s_pot_en.xvg' % filename)
    b= np.loadtxt('1et_%s_kin_en.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    
    t2=b[:,0]
    y2=b[:,1]
    plt.plot()
    plt.plot(t1, y1, "b-", t2, y2, "r-" )
    red_patch = mpatches.Patch(color='red', label='Kinetic')
    blue_patch = mpatches.Patch(color='blue', label='Potential')
    plt.legend(handles=[red_patch,blue_patch])
    plt.title('Energies of %s system' % filename)
In [63]:
for filename in ['sd']:
    a= np.loadtxt('1et_%s_pot_en.xvg' % filename)
    b= np.loadtxt('1et_%s_kin_en.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    
    t2=b[:,0]
    y2=b[:,1]
    plt.plot()
    plt.plot(t1, y1, "b-", t2, y2, "r-" )
    red_patch = mpatches.Patch(color='red', label='Kinetic')
    blue_patch = mpatches.Patch(color='blue', label='Potential')
    plt.legend(handles=[red_patch,blue_patch])
    plt.title('Energies of %s system' % filename)

Рассмотрим распределение длинны связи С-С за время моделирования.

In [65]:
import subprocess
for i in ['be','vr','nh','an','sd']:
    cmd = 'g_bond -f et_%s.tpr.trr -s et_%s.tpr -o bond_%s.xvg -n b.ndx -xvg none' % (i,i,i)
    subprocess.call(cmd,shell=True)
In [70]:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
for filename in ['be']:
    a= np.loadtxt('bond_%s.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    width = 0.0001 
    plt.bar(t1,y1,width, color="blue")
    plt.title('Length of C-C bond in %s system' % filename)
In [71]:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
for filename in ['vr']:
    a= np.loadtxt('bond_%s.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    width = 0.0001 
    plt.bar(t1,y1,width, color="blue")
    plt.title('Length of C-C bond in %s system' % filename)
In [72]:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
for filename in ['nh']:
    a= np.loadtxt('bond_%s.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    width = 0.0001 
    plt.bar(t1,y1,width, color="blue")
    plt.title('Length of C-C bond in %s system' % filename)
In [74]:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
for filename in ['an']:
    a= np.loadtxt('bond_%s.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    width = 0.0001 
    plt.bar(t1,y1,width, color="blue")
    plt.title('Length of C-C bond in %s system' % filename)
In [75]:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
for filename in ['sd']:
    a= np.loadtxt('bond_%s.xvg' % filename)
    t1=a[:,0]
    y1=a[:,1]
    width = 0.0001 
    plt.bar(t1,y1,width, color="blue")
    plt.title('Length of C-C bond in %s system' % filename)

По форме на распределение Больцмана методы мало похожи. Максимумы тоже не совпадает с 1.53, кроме sd.

In [77]:
import subprocess
for filename in ['be','vr','nh','an','sd']:
    cmd1 = 'grompp -f %s.mdp -c etane.gro -p et.top -o et_%s.tpr >& log.grompp' %(filename,filename)
    cmd2 = 'mdrun -deffnm et_%s.tpr -v -nt 1' %filename
    output_file = open(filename+'.sh','w')
    output_file.writelines('\n'.join([cmd1,cmd2]))
    output_file.close()
In [78]:
%%bash
chmod +x *.sh
./be.sh
./vr.sh
./nh.sh
./an.sh
./sd.sh

                         :-)  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_be.tpr  Input        Run input file: tpr tpb tpa
  -o  et_be.tpr.trr  Output       Full precision trajectory: trr trj cpt
  -x  et_be.tpr.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  et_be.tpr.cpt  Input, Opt.  Checkpoint file
-cpo  et_be.tpr.cpt  Output, Opt. Checkpoint file
  -c  et_be.tpr.gro  Output       Structure file: gro g96 pdb etc.
  -e  et_be.tpr.edr  Output       Energy file
  -g  et_be.tpr.log  Output       Log file
-dhdl et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
-field  et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
-table  et_be.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tablep  et_be.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tableb  et_be.tpr.xvg  Input, Opt.  xvgr/xmgr file
-rerun  et_be.tpr.trr  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi  et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
-tpid et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
 -ei  et_be.tpr.edi  Input, Opt.  ED sampling input
 -eo  et_be.tpr.edo  Output, Opt. ED sampling output
  -j  et_be.tpr.gct  Input, Opt.  General coupling stuff
 -jo  et_be.tpr.gct  Output, Opt. General coupling stuff
-ffout  et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
-devout  et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
-runav  et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
 -px  et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
 -pf  et_be.tpr.xvg  Output, Opt. xvgr/xmgr file
-mtx  et_be.tpr.mtx  Output, Opt. Hessian matrix
 -dn  et_be.tpr.ndx  Output, Opt. Index file
-multidir et_be.tpr  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.tpr  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.tpr.log to ./#et_be.tpr.log.1#
Getting Loaded...
Reading file et_be.tpr, VERSION 4.5.5 (single precision)
Loaded with Money


Back Off! I just backed up et_be.tpr.trr to ./#et_be.tpr.trr.1#

Back Off! I just backed up et_be.tpr.edr to ./#et_be.tpr.edr.1#
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.tpr.gro to ./#et_be.tpr.gro.1#
step 250000, remaining runtime:     0 s          
               NODE (s)   Real (s)      (%)
       Time:      3.970      4.179     95.0
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      0.000    375.990   5440.828      0.004

gcq#43: "May the Force Be With You" (Star Wars)

                         :-)  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_vr.tpr  Input        Run input file: tpr tpb tpa
  -o  et_vr.tpr.trr  Output       Full precision trajectory: trr trj cpt
  -x  et_vr.tpr.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  et_vr.tpr.cpt  Input, Opt.  Checkpoint file
-cpo  et_vr.tpr.cpt  Output, Opt. Checkpoint file
  -c  et_vr.tpr.gro  Output       Structure file: gro g96 pdb etc.
  -e  et_vr.tpr.edr  Output       Energy file
  -g  et_vr.tpr.log  Output       Log file
-dhdl et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
-field  et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
-table  et_vr.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tablep  et_vr.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tableb  et_vr.tpr.xvg  Input, Opt.  xvgr/xmgr file
-rerun  et_vr.tpr.trr  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi  et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
-tpid et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
 -ei  et_vr.tpr.edi  Input, Opt.  ED sampling input
 -eo  et_vr.tpr.edo  Output, Opt. ED sampling output
  -j  et_vr.tpr.gct  Input, Opt.  General coupling stuff
 -jo  et_vr.tpr.gct  Output, Opt. General coupling stuff
-ffout  et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
-devout  et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
-runav  et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
 -px  et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
 -pf  et_vr.tpr.xvg  Output, Opt. xvgr/xmgr file
-mtx  et_vr.tpr.mtx  Output, Opt. Hessian matrix
 -dn  et_vr.tpr.ndx  Output, Opt. Index file
-multidir et_vr.tpr  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.tpr  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.tpr.log to ./#et_vr.tpr.log.1#
Getting Loaded...
Reading file et_vr.tpr, VERSION 4.5.5 (single precision)
Loaded with Money


Back Off! I just backed up et_vr.tpr.trr to ./#et_vr.tpr.trr.1#

Back Off! I just backed up et_vr.tpr.edr to ./#et_vr.tpr.edr.1#
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.tpr.gro to ./#et_vr.tpr.gro.1#
step 250000, remaining runtime:     0 s          
               NODE (s)   Real (s)      (%)
       Time:      4.040      4.292     94.1
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      0.000    369.384   5346.556      0.004

gcq#251: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)

                         :-)  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.

                                :-)  mdrun  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -s      et_nh.tpr  Input        Run input file: tpr tpb tpa
  -o  et_nh.tpr.trr  Output       Full precision trajectory: trr trj cpt
  -x  et_nh.tpr.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  et_nh.tpr.cpt  Input, Opt.  Checkpoint file
-cpo  et_nh.tpr.cpt  Output, Opt. Checkpoint file
  -c  et_nh.tpr.gro  Output       Structure file: gro g96 pdb etc.
  -e  et_nh.tpr.edr  Output       Energy file
  -g  et_nh.tpr.log  Output       Log file
-dhdl et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
-field  et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
-table  et_nh.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tablep  et_nh.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tableb  et_nh.tpr.xvg  Input, Opt.  xvgr/xmgr file
-rerun  et_nh.tpr.trr  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi  et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
-tpid et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
 -ei  et_nh.tpr.edi  Input, Opt.  ED sampling input
 -eo  et_nh.tpr.edo  Output, Opt. ED sampling output
  -j  et_nh.tpr.gct  Input, Opt.  General coupling stuff
 -jo  et_nh.tpr.gct  Output, Opt. General coupling stuff
-ffout  et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
-devout  et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
-runav  et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
 -px  et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
 -pf  et_nh.tpr.xvg  Output, Opt. xvgr/xmgr file
-mtx  et_nh.tpr.mtx  Output, Opt. Hessian matrix
 -dn  et_nh.tpr.ndx  Output, Opt. Index file
-multidir et_nh.tpr  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.tpr  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.tpr.log to ./#et_nh.tpr.log.1#
Getting Loaded...
Reading file et_nh.tpr, VERSION 4.5.5 (single precision)
Loaded with Money


Back Off! I just backed up et_nh.tpr.trr to ./#et_nh.tpr.trr.1#

Back Off! I just backed up et_nh.tpr.edr to ./#et_nh.tpr.edr.1#
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.tpr.gro to ./#et_nh.tpr.gro.1#
step 250000, remaining runtime:     0 s          
               NODE (s)   Real (s)      (%)
       Time:      4.010      4.233     94.7
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      0.000    372.196   5386.556      0.004

gcq#94: "Exactly" (Pulp Fiction)

                         :-)  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_an.tpr  Input        Run input file: tpr tpb tpa
  -o  et_an.tpr.trr  Output       Full precision trajectory: trr trj cpt
  -x  et_an.tpr.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  et_an.tpr.cpt  Input, Opt.  Checkpoint file
-cpo  et_an.tpr.cpt  Output, Opt. Checkpoint file
  -c  et_an.tpr.gro  Output       Structure file: gro g96 pdb etc.
  -e  et_an.tpr.edr  Output       Energy file
  -g  et_an.tpr.log  Output       Log file
-dhdl et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
-field  et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
-table  et_an.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tablep  et_an.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tableb  et_an.tpr.xvg  Input, Opt.  xvgr/xmgr file
-rerun  et_an.tpr.trr  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi  et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
-tpid et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
 -ei  et_an.tpr.edi  Input, Opt.  ED sampling input
 -eo  et_an.tpr.edo  Output, Opt. ED sampling output
  -j  et_an.tpr.gct  Input, Opt.  General coupling stuff
 -jo  et_an.tpr.gct  Output, Opt. General coupling stuff
-ffout  et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
-devout  et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
-runav  et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
 -px  et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
 -pf  et_an.tpr.xvg  Output, Opt. xvgr/xmgr file
-mtx  et_an.tpr.mtx  Output, Opt. Hessian matrix
 -dn  et_an.tpr.ndx  Output, Opt. Index file
-multidir et_an.tpr  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.tpr  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.tpr.log to ./#et_an.tpr.log.1#
Getting Loaded...
Reading file et_an.tpr, VERSION 4.5.5 (single precision)
Loaded with Money


Back Off! I just backed up et_an.tpr.trr to ./#et_an.tpr.trr.1#

Back Off! I just backed up et_an.tpr.edr to ./#et_an.tpr.edr.1#
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.tpr.gro to ./#et_an.tpr.gro.1#
step 250000, remaining runtime:     0 s          
               NODE (s)   Real (s)      (%)
       Time:      3.890      4.189     92.9
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      0.000    383.839   5552.722      0.004

gcq#188: "Clickety Clickety Click" (System Manager From Hell)

                         :-)  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_sd.tpr  Input        Run input file: tpr tpb tpa
  -o  et_sd.tpr.trr  Output       Full precision trajectory: trr trj cpt
  -x  et_sd.tpr.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  et_sd.tpr.cpt  Input, Opt.  Checkpoint file
-cpo  et_sd.tpr.cpt  Output, Opt. Checkpoint file
  -c  et_sd.tpr.gro  Output       Structure file: gro g96 pdb etc.
  -e  et_sd.tpr.edr  Output       Energy file
  -g  et_sd.tpr.log  Output       Log file
-dhdl et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
-field  et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
-table  et_sd.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tablep  et_sd.tpr.xvg  Input, Opt.  xvgr/xmgr file
-tableb  et_sd.tpr.xvg  Input, Opt.  xvgr/xmgr file
-rerun  et_sd.tpr.trr  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi  et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
-tpid et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
 -ei  et_sd.tpr.edi  Input, Opt.  ED sampling input
 -eo  et_sd.tpr.edo  Output, Opt. ED sampling output
  -j  et_sd.tpr.gct  Input, Opt.  General coupling stuff
 -jo  et_sd.tpr.gct  Output, Opt. General coupling stuff
-ffout  et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
-devout  et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
-runav  et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
 -px  et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
 -pf  et_sd.tpr.xvg  Output, Opt. xvgr/xmgr file
-mtx  et_sd.tpr.mtx  Output, Opt. Hessian matrix
 -dn  et_sd.tpr.ndx  Output, Opt. Index file
-multidir et_sd.tpr  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.tpr  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.tpr.log to ./#et_sd.tpr.log.1#
Getting Loaded...
Reading file et_sd.tpr, VERSION 4.5.5 (single precision)
Loaded with Money


Back Off! I just backed up et_sd.tpr.trr to ./#et_sd.tpr.trr.1#

Back Off! I just backed up et_sd.tpr.edr to ./#et_sd.tpr.edr.1#
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.tpr.gro to ./#et_sd.tpr.gro.1#
step 250000, remaining runtime:     0 s          
               NODE (s)   Real (s)      (%)
       Time:      4.580      4.861     94.2
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      0.000    339.158   4716.176      0.005

gcq#31: "With a Little Penknife" (Nick Cave)
In [1]:
from IPython.display import Image
Image(filename='time.png')
Out[1]:

Из данной таблицы можно сделать вывoд, что самым быстрым является метод be.