On Sat, Jun 15, 2013 at 9:00 PM, Cuiying Jian <[email protected]>wrote:
> > > > > > > > > > Hi Mark, > > I test the simulations again using Berendsen thermostat -- Still, I cannot > get binary identical results. > I do two sets of simulations: > 1. Use Gromacs 4.5.2 installed on my personal computer: > 4.6.2, I hope. Nobody is interested in reports about 4.5.2 :-) > Run 2 simulations using the command: mdrun -s md.tpr -deffnm md -nt 1 -cpt > 0 -reprod (-nt 1 ensures that the number of threads to start is > 1).Terminate one simulation manually.Restart this simulation by: mdrun -s > md.tpr -deffnm md -nt 1 -cpt 0 -cpi md.cpt -reprod -npme 0 (-npme o ensures > that the number of pme nodes for the restarting the same with that in the > checkpoint file.)Compare the results with those from continuous ones. What does gmxcheck say when comparing the resulting ostensibly equivalent trajectory files? Please provide a snippet of output if it says things differ. We want to see how big "different" is. Also the top 20 lines of a .log file. Also, you can do the above procedure in a controlled manner in 4.6.2 by using mdrun -nsteps on the run you wish to stop prematurely. Might your FFT library be multi-threading behind your back? Mark 2. Use Gromacs 4.0.7 installed on a cluster (only one processor is used > during the simulation): > Run 2 simulations using the command: mdrun_s -v -cpt 0 -s md.tpr -deffnm > md -reprod Terminate one simulation manually.Restart this simulation by: > mdrun_s -v -cpt 0 -cpi md.cpt -s md.tpr -deffnm md -reprod Compare the > results with those from continuous ones. Still, I cannot get binary > identical results. As mentioned ealier, the only case I can get binary > identical results is for SPC rigid water molecules (using velocity > rescaling thermostat in Gromacs 4.0.7). I guess that the reason for this > problem may also be caused by the LINCS algorithm used to constraint all > bonds in other cases except the rigid water case.. Thanks a lot. > Cheers,Cuiying > > > Date: Mon, 3 Jun 2013 19:15:12 +0200 > > From: Mark Abraham <[email protected]> > > Subject: Re: [gmx-users] RE: About the binary identical results by > > restarting from the checkpoint file > > To: Discussion list for GROMACS users <[email protected]> > > Message-ID: > > <CAMNuMARBEZ=m=Y_M1= > [email protected]> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > On Mon, Jun 3, 2013 at 6:59 PM, Cuiying Jian <[email protected] > >wrote: > > > > > 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 > > > > > > > This is not generally enough to generate a serial run in 4.6, by the way. > > GROMACS tries very hard to automatically use all the resources available > in > > the best way. See mdrun -h for various -nt* options, and consult the > > pre-step-0 part of the .log file for feedback. > > > > 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 > > > > > > > This coupling algorithm has a stochastic component, and at least at some > > points in history the random number generator was either not checkpointed > > properly, or not propagated in parallel properly. I'm not sure offhand if > > any of that has been fixed yet (I doubt it), but you can test (parts of) > > this hypothesis by using Berendsen (in any GROMACS 4.x), or really being > > sure you've run a single thread. > > > > If Berendsen is fully reproducible, then the RNG is the issue. While > that's > > irritating, it probably won't get fixed before GROMACS 5 (as a side > effect > > of other stuff going on). > > > > Mark > > > > 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 > > > > > > > > > ------------------------------ > > > > -- > > 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! > > > > End of gmx-users Digest, Vol 110, Issue 16 > > ****************************************** > > > > > -- > 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? 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