Hi Mark, Sorry for my carelessness. I check my email again and see your reply. I get your point that my problem may be (at least part of) caused by RNG of the thermostat. Thanks again and sorry for my careless bothering. Cheers, Cuiying > On Fri, Jun 14, 2013 at 12:52 AM, Cuiying Jian > <[email protected]>wrote: > > > 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 > > > > I answered you 11 days ago and you are re-posting with nothing new. Why? > > Mark > > > > > > > > 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
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
