[gmx-users] RE: About the binary identical results by restarting from the checkpoint file
Cuiying Jian
cuiying_jian at hotmail.com
Fri Jun 14 18:26:30 CEST 2013
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 <cuiying_jian at hotmail.com>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: cuiying_jian at hotmail.com
> > To: gmx-users at gromacs.org
> > 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 <cuiying_jian at hotmail.com
> > >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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