Hi GROMACS Users, I am sorry if you are bothered by my second post about this topic. But the fact is that I tested restarting simulations with .cpt files by GROMACS 4.6.1. and I still cannot get binary identical results from restarted simulations with those from continuous simulations. The command I used for restarting is as the following (e.g., only one processor is used during the simulations.): mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod For further information, I attach my original .mdp file below: constraints = all-bonds ; convert all bonds to constraints. integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 2 ns. nstcomm = 10 ; frequency for center of mass motion removal. nstxout = 5 ; collect data every 10.0 ps. nstxtcout = 5 ; frequency to write coordinate to xtc trajectory. nstvout = 5 ; frequency to write velocities to output trajectory. nstfout = 5 ; frequency to write forces to output trajectory. nstlog = 5 ; frequency to write energies to log file. nstenergy = 5 ; frequency to write energies to energy file. nstlist = 1 ; frequency to update the neighbor list. ns_type = grid rlist = 1.4 coulombtype = PME rcoulomb = 1.4 vdwtype = cut-off rvdw = 1.4 pme_order = 8 ; use 6,8 or 10 when running in parallel ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; don't apply any correction ;open LINCS constraint_algorithm = LINCS lincs_order = 4 ;highest order in the expansion of the constraint coupling matrix lincs_warnangle = 30 ;maximum angle that a bond can rotate before LINCS will complain lincs_iter = 1 ;number of iterations to correct for a rotational lengthening in LINCS ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps = HEP ref_t = 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; generate velocity is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 Is there something wrong with my .mdp file or my command? Thanks a lot. Cheers, Cuiying From: [email protected] To: [email protected] Subject: RE: About the binary identical results by restarting from the checkpoint file Date: Mon, 3 Jun 2013 16:59:31 +0000
Hi Mark, Thanks for your reply. I tested restarting simulations with .cpt files by GROMACS 4.6.1. and the problems are still there, i.e. I cannot get binary identical results from restarted simulations with those from continuous simulations. The command I used for restarting is as the following (Only one processor is used during the simulations.): mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod For further information, I attach my original .mdp file below: constraints = all-bonds ; convert all bonds to constraints. integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 2 ns. nstcomm = 10 ; frequency for center of mass motion removal. nstxout = 5 ; collect data every 10.0 ps. nstxtcout = 5 ; frequency to write coordinate to xtc trajectory. nstvout = 5 ; frequency to write velocities to output trajectory. nstfout = 5 ; frequency to write forces to output trajectory. nstlog = 5 ; frequency to write energies to log file. nstenergy = 5 ; frequency to write energies to energy file. nstlist = 1 ; frequency to update the neighbor list. ns_type = grid rlist = 1.4 coulombtype = PME rcoulomb = 1.4 vdwtype = cut-off rvdw = 1.4 pme_order = 8 ; use 6,8 or 10 when running in parallel ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; don't apply any correction ;open LINCS constraint_algorithm = LINCS lincs_order = 4 ;highest order in the expansion of the constraint coupling matrix lincs_warnangle = 30 ;maximum angle that a bond can rotate before LINCS will complain lincs_iter = 1 ;number of iterations to correct for a rotational lengthening in LINCS ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps = HEP ref_t = 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; generate velocity is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 Is there something wrong with my .mdp file or my command? Thanks a lot. Cheers, Cuiying > On Sun, Jun 2, 2013 at 10:37 PM, Cuiying Jian <[email protected]>wrote: > > > Hi GROMACS Users, > > > > These days, I am testing restarting simulaitions with .cpt files. I > > already set nlist=1 in the .mdp file. I can restart my simulations (which > > are stopped manually) with the following commands (version 4.0.7): > > mpiexec mdrun_s_mpi -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod > > -reprod is used to force binary identical simulaitons. > > > > During the restarted simulations, same number of processors are used as > > that in the simulation interrupted. The only case, in which I can get > > binary identical results with those from the continuous simulations (which > > are not stopped manually), is for SPC water molecules. Any other molecules > > (like -heptane), I can never get binary identical results with those from > > the continuous simulations. > > > > I also try to get new .tpr files by: > > tpbconv_s -s md.tpr -f md.trr -e md.edr -c md_c.tpr -cont > > and then: > > mpiexec mdrun_s_mpi -v -s md_c.tpr -cpt 0 -cpi md.cpt -deffnm md_c -reprod > > But I still cannot get binary identical results. > > > > I also test the simulations with only one processor and binary identical > > results are still not obtained. Using double precision does not solve the > > problems. > > > > I think that the above problems are caused by some information may not be > > stored during the running of the simulations. > > > > That seems likely. The leading candidate would be a random number generator > you're using for a stochastic integrator. Your .mdp file would have been > useful. > > On the other hand, if I run two independent simulations using the exactly > > same number of processors, the same commands and the same input files, i.e. > > mpiexec mdrun_s_mpi -v -s md.tpr -deffnm md -reprod > > I can always get binary identical results from these two independent > > simulations. > > > > I understand that MD is chaotic and if we run simulation for enough long > > time, simulation results should converge. Also, there are factors which may > > affect the reproducibility as described in the GROMACS website. But for my > > purpose, I am curious about whether there are certain methods through which > > I can get binary identical results from restarted simulations and > > continuous simulations. Thanks a lot. > > > > There are ways to be fully reproducible, but probably not every combination > of algorithms has that property. 4.0.7 is so old no problem will be fixed, > unless it can also be shown in 4.6 ;-) > > Mark
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