Re: [gmx-users] output of the -hist option of the g_wham command
Hi, It simply gives you the histogram of each individual input simulation for the umbrella. From my experience, it is very useful in cases that you're WHAM will not converge and it allows you to verify weather there is a sufficient overlap between adjacent input configurations.It can be useful in choosing the parameters for the Umbrella force constant and the initial separation between the configurations. Good luck! amir On Tue, Jun 22, 2010 at 11:55 PM, Ozge Engin ozge.en...@gmail.com wrote: Hi all, I am trying to perform umbrella sampling along with the WHAM to get the PMF. I go over the umbrella sampling tutorial prepared by Justin. Everything seems OK to me except one point. I could not understand the output given by the hist option of the g_wham command. There, what does histogram of configurations mean? Thank you -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in parallel mdrun
Hi Gavin, I had exactly the same problem a few days ago. you have 2 options for parallel runs: domain decomposition (default) and particle decomposition you can either try to manipulate the parameters of your system such that they fit domain decomposition or choose the easier way..that is using particle decomposition (mdrun -pd) i use it and it works fine, though I'm not sure it the most efficient algorithm for parallel runs. Cheers, Amir On Tue, Jun 22, 2010 at 6:58 PM, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi all I have a ran a simulation of 64 molecules in a cubic box with side 6 nm, using nose-hoover thermostat, parinello-rahman pressure coupling, and pme. Runnin the simulation in parallel is no problem (using 16 CPUs). However when I want to run an almost identical molecule using the exact same conditions as the previous case I get the following error (below), until eventual I reduce the number of CPUs to 4 and then everything is fine. I would however like to run the simulation using more processors if anyone can give me some advise. Note the following error is from the log file. *Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 5888 Fatal error: There is no domain decomposition for 13 nodes that is compatible with the given box and a minimum cell size of 1.25784 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems with installing mpi-version of Gromacs
Dear All:
I have installed Gromacs on a Linux (RedHat) cluster, using the following csh
script -
-
#! /bin/csh
set DIR=/private/gnss/Gromacs
setenv SOFT ${DIR}/software
setenv CPPFLAGS -I$SOFT/include
setenv LDFLAGS -L$SOFT/lib
setenv NCPU 4
setenv PATH $PATH:$SOFT/bin
cd openmpi-1.2.8; ./configure --prefix=$SOFT; make -j $NCPU; make install
cd ../fftw-3.1.3; ./configure --prefix=$SOFT --enable-float; make -j $NCPU;
make install
cd ../gsl-1.11; ./configure --prefix=$SOFT; make -j $NCPU; make install
cd ../gromacs-4.0.7; ./configure --prefix=$SOFT --with-gsl; make -j $NCPU; make
install
make distclean; ./configure --prefix=$SOFT --program-suffix=_mpi --enable-mpi
--with-gsl; make mdrun -j $NCPU; make install-mdrun
-
It seemed to have worked OK, and we could run Gromacs on a single processor.
When I tried to create a parallel version with the script -
-
#! /bin/csh
set DIR=/private/gnss/Gromacs
setenv SOFT ${DIR}/software
setenv CPPFLAGS -I$SOFT/include
setenv LDFLAGS -L$SOFT/lib
setenv NCPU 4
setenv PATH $PATH:$SOFT/bin
cd gromacs-4.0.7; ./configure --prefix=$SOFT --with-gsl --enable-mpi; make -j
$NCPU mdrun; make install-mdrun
-
- the installation log ended with -
.
checking whether the MPI cc command works... configure: error: Cannot compile
and link MPI code with mpicc
make: *** No rule to make target `mdrun'. Stop.
make: *** No rule to make target `install-mdrun'. Stop.
I can't figure out from this message what is wrong or missing with my MPI.
Can anyone help?
Thanks a lot in advance for your help
Pinchas
Dr. Pinchas Aped Tel.:(+972-3) 531-7683
Department of ChemistryFAX : (+972-3) 738-4053
Bar-Ilan University E-Mail:a...@mail.biu.ac.il
Ramat-Gan 52900, ISRAEL WWW: http://www.biu.ac.il/~aped
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[gmx-users] (no subject)
Hellow, My sequence was processed with SPDBV which add NH3 and COO- at the Nterminal and Cterminal respectively thereby MD simulation was carried out using GROMACS versions of 3.3.2 and 4.0. The system was working well. Now I would like to add protecting groups i.e.acetyl group (CH3CO) and Nmethyl (NHCH3) at the N and C terminal respectively instead of NH3 and COO- using Gromacs 4.0. Kindly suggest me needful action for the said construction. Or kindly suggest the software which can construct like CH3CO-Gly-trp-lys- - - - - - - - NHCH3 thereby getting output file can be used by GROMACS 4.o for completing my MD of the molecuel having such a sequence any like CH3CO-Gly-trp-lys- - - - - - - - NHCH3 . M. Baskar e.mail:munu...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error in MD simulation
Dear Gromacs users, First I have to mention few points. I read all the LINCS error and tried a number of options. 1, Minimized well the system. and the Epot and Max Forces are very resonable. Steepest Descents converged to Fmax 100 in 379 steps Potential Energy = -1.0573750e+05 Maximum force = 8.0876366e+01 on atom 1117 Norm of force = 8.7360611e+00 2, Equlibrate well the system. It works for 100ps Once I run NPT simulation using the following .mdp parameter set it shows the following error. ; The etire lines starting with ';' ARE COMMENTS title = NPT equilibration using the berendsen thermostat and barostat ; Title of run cpp = /usr/bin/cpp ; location of cpp on linux ; The following lines tell the program the standard locations where to find certain files ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too ; RUN CONTROL PARAMETERS integrator = md ; leap-frog integrator ; Start time and timestep in ns tinit= 0 dt = 0.002 ; 2fs nsteps = 50 ; 2*500 = 1ns ; THOSE OPTIONS REMOVE MOTION OF THE ASPHALTENE MODEL COMPUNDS RELATIVE TO THE SOLVENT/IONS ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= System ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 200 emstep = 0.01 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 2000 nstvout = 2000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = BIS HEP ; Selection of energy groups energygrps = BIS HEP ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz ; nblist cut-off rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb = 1.2 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; account for the cut-off vdw scheme ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.16 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling is on tcoupl = V-rescale; modified berendsen thermostat ; Groups to couple separately tc-grps = BIS HEP ; three coupling gropus ; Time constant (ps) and reference temperature (K) tau-t= 0.1 0.1 ; time constant ref-t= 298 298 ; reference temprature ; Pressure coupling is on Pcoupl = berendsen; Pressure coupling is on Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 3 3 compressibility = 1.47e-4 1.47e-4 ; isothermal compressibility, bar^-1 ref-p= 1 1 ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes ; assign velocities from Maxwell distribution (MXD) gen-temp = 298 ; temperature for MXD gen-seed = 173529; used to initialize random generator for random velocities ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For
Re: [gmx-users] Error in MD simulation
- Original Message - From: tekle...@ualberta.ca Date: Monday, June 28, 2010 6:01 Subject: [gmx-users] Error in MD simulation To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Dear Gromacs users, First I have to mention few points. I read all the LINCS error and tried a number of options. 1, Minimized well the system. and the Epot and Max Forces are very resonable. Steepest Descents converged to Fmax 100 in 379 steps Potential Energy = -1.0573750e+05 Maximum force = 8.0876366e+01 on atom 1117 Norm of force = 8.7360611e+00 2, Equlibrate well the system. It works for 100ps Once I run NPT simulation using the following .mdp parameter set it shows the following error. ; The etire lines starting with ';' ARE COMMENTS title = NPT equilibration using the berendsen thermostat and barostat ; Title of run cpp = /usr/bin/cpp ; location of cpp on linux ; The following lines tell the program the standard locations where to find certain files ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too ; RUN CONTROL PARAMETERS integrator = md ; leap-frog integrator ; Start time and timestep in ns tinit= 0 dt = 0.002 ; 2fs nsteps = 50 ; 2*500 = 1ns ; THOSE OPTIONS REMOVE MOTION OF THE ASPHALTENE MODEL COMPUNDS RELATIVE TO THE SOLVENT/IONS ; mode for center of mass motion removal comm- mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm- grps= System ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd- fric = 0 ld- seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 200 emstep = 0.01 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 2000 nstvout = 2000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc- precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc- grps = BIS HEP ; Selection of energy groups energygrps = BIS HEP ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns- type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz ; nblist cut-off rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb = 1.2 ; Method for doing Van der Waals vdw- type = Cut-off ; cut-off lengths rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; account for the cut-off vdw scheme ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.16 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling is on tcoupl = V-rescale; modified berendsen thermostat ; Groups to couple separately tc- grps = BIS HEP ; three coupling gropus ; Time constant (ps) and reference temperature (K) tau- t= 0.1 0.1 ; time constant ref- t= 298 298 ; reference temprature ; Pressure coupling is on Pcoupl = berendsen; Pressure coupling is on Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau- p= 3 3 compressibility = 1.47e-4 1.47e-4 ; isothermal compressibility, bar^-1 ref- p= 1 1 ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen- vel = yes ; assign velocities from Maxwell distribution (MXD) gen- temp = 298 ; temperature for MXD gen- seed = 173529; used to initialize random generator for random velocities ;
Re: [gmx-users] Problems with installing mpi-version of Gromacs
- Original Message -
From: Pinchas Aped a...@mail.biu.ac.il
Date: Monday, June 28, 2010 3:43
Subject: [gmx-users] Problems with installing mpi-version of Gromacs
To: Discussion list for GROMACS users gmx-users@gromacs.org
---
|
Dear All: I have installed Gromacs on a Linux (RedHat) cluster, using
the following csh script -
-
#! /bin/csh set DIR=/private/gnss/Gromacs setenv SOFT
${DIR}/software
setenv CPPFLAGS -I$SOFT/include
setenv LDFLAGS -L$SOFT/lib
setenv NCPU 4
setenv PATH $PATH:$SOFT/bin
cd openmpi-1.2.8; ./configure --prefix=$SOFT; make -j $NCPU; make install
cd ../fftw-3.1.3; ./configure --prefix=$SOFT --enable-float; make -j $NCPU;
make install
cd ../gsl-1.11; ./configure --prefix=$SOFT; make -j $NCPU; make install
cd ../gromacs-4.0.7; ./configure --prefix=$SOFT --with-gsl; make -j $NCPU;
make install
make distclean; ./configure --prefix=$SOFT --program-suffix=_mpi
--enable-mpi --with-gsl; make mdrun -j $NCPU; make install-mdrun
-
It seemed to have worked OK, and we could run Gromacs on a single
processor. When I tried to create a parallel version with the script -
-
#! /bin/csh set DIR=/private/gnss/Gromacs setenv SOFT
${DIR}/software
setenv CPPFLAGS -I$SOFT/include
setenv LDFLAGS -L$SOFT/lib
setenv NCPU 4
setenv PATH $PATH:$SOFT/bin cd gromacs-4.0.7; ./configure
--prefix=$SOFT --with-gsl --enable-mpi; make -j $NCPU mdrun; make
install-mdrun
-
- the installation log ended with - . checking
whether the MPI cc command works... configure: error: Cannot compile and
link MPI code with mpicc
make: *** No rule to make target `mdrun'. Stop.
make: *** No rule to make target `install-mdrun'. Stop. I can't
figure out from this message what is wrong or missing with my MPI.
It looks like you included the scripts the wrong way around, or something.
Both scripts should build MPI-enabled mdrun, with the second not naming it with
_mpi. See
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions
for the usual procedure.
You can inspect the last 100 or so lines of config.log to see the actual error
issue.
The issue has probably got nothing to do with GROMACS. Try compiling and
running some MPI test program to establish this.
Mark
|
---
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Re: [gmx-users] (no subject)
- Original Message - From: munu...@yahoo.com Date: Monday, June 28, 2010 5:29 Subject: [gmx-users] (no subject) To: gmx-users@gromacs.org --- | Hellow, My sequence was processed with SPDBV which add NH3 and COO- at the Nterminal and Cterminal respectively thereby MD simulation was carried out using GROMACS versions of 3.3.2 and 4.0. The system was working well. Now I would like to add protecting groups i.e.acetyl group (CH3CO) and Nmethyl (NHCH3) at the N and C terminal respectively instead of NH3 and COO- using Gromacs 4.0. Kindly suggest me needful action for the said construction. Or kindly suggest the software which can construct like CH3CO-Gly-trp-lys- - - - - - - - NHCH3 thereby getting output file can be used by GROMACS 4.o for completing my MD of the molecuel having such a sequence any like CH3CO-Gly-trp-lys- - - - - - - - NHCH3 . | --- You will need some non-GROMACS software to do this. Some suggestions are here http://www.gromacs.org/Documentation/File_Formats/Coordinate_File Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] [ dihedraltypes ]
- Original Message - From: akram gorji lotus6...@gmail.com Date: Sunday, June 27, 2010 6:56 Subject: [gmx-users] [ dihedraltypes ] To: gmx-users gmx-users@gromacs.org Hi everyone According to OPLS-AA force field, I want to complete section of [ dihedraltypes ] in ff… bon.itp between 4 atoms (carbonyl C , Benzene C , Benzene C , Benzene H ) and also (carbonyl C , Benzene C , Benzene C , Benzene C )for the structure of Benzoic acid . Can you help me? Thank you You'll need to do some homework in the forcefield files to find out the OPLS/AA atom types for these atoms, and whether any of the existing dihedral types are appropriate here. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_anaeig -proj
Carla: Agreed that this can be confusing. What you seem to want can be obtained with g_anaeig -filt Nevertheless, What you get with -proj can also be very useful. For a very quick overview: -filt will output a .xtc file that contains only those motions that are along the selected EVs. Separately, -proj can project the trajectory down into an N-dimensional space for N selected EV's... I think that if you had followed the tutorial further and made the xmgrace plot (with both 1st and 2ns EVs) as the tutorial suggests, then you might have had a better chance to understand this part. ### Tsjerk: First, great tutorial, I hadn't seen this before. Second, you might avoid this type of confusion by mentioning during the command: g_anaeig -s ../topol.tpr -f ../traj.xtc -v eigenvectors.trr -eig eigenvalues.xvg -proj proj-ev1.xvg -extr ev1.pdb -rmsf rmsf-ev1.xvg -first 1 -last 1 that you care actually doing a few things at once... or perhaps actually break the command apart into separate g_anaeig -proj and g_anaeig -extr calls. ### All: might it be a good idea to get the html addresses of nice tutorials into the output messages of the analysis tools? Chris -- original message -- Hi everyone, please I'm doing for the first time a covariance analysis. I followed this tutorial: http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.htmlhttp://nmr.chem.uu.nl/%7Etsjerk/course/molmod/analysis1.html But I don't understand. -proj gives the projection of the trajectory on the first eigenvector, so I was expecting to have new coordinates for each atom or each residue. Instead, I get a .xvg file saying: projection on eigenvectors (nm) @ xaxis label Time (ps) yaxis label vec 1 Please can anyone tell me what this actually means? What data is in nanometers? What does gromacs project? Sorry if my question is stupid, but I can't find the answer. Thank you. Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Diffusion constant
Dear Users I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way: Obtaining a continuos trajectory 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc Obtaining the msd of the solute, removing the center of mass of the system Firt way: 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm I choose SOLUTE Second way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv I choose SOLUTE There are significative differences in the results? according to the gromacs manual -mv option is used in molecules, What is the correct step, 2a or 2b? Regards Teobaldo ___Teobaldo Ricardo Cuya Guizado, Msc.Physics DepartmentPontificia Universidade Catolica de Rio de JaneiroRua Marquês de São Vicente, 22522451-900 Gávea - Rio de Janeiro - RJ BRASILPhone: 55-21-7613-3843e-mail: trcu...@gmail.comweb page: http://www.trcuyag.blogspot.com___ _ Jeux Messenger : mettez vos amis au défi! http://go.microsoft.com/?linkid=9734397-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate the energy drift?
Hi all Gromacs users: In Gromacs 4 paper GROMACS 4 Algorithms for Highly Efficient,Load-Balanced, and Scalable Molecular Simulation The energy drift for GROMACS is 0.01 kBT/ns per degree of freedom. But I don't know how to calculate the value of energy drift. Is this energy the kinetic energy or the sum of kinetic and potential energies? And if the simulation runs 20ns, is the energy drift the value of energy difference between first and last step divided by the simulation time (20ns)? Appreciate for any help in advance! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
