[gmx-users] RE: About the binary identical results by restarting from the checkpoint file
Mark Abraham
mark.j.abraham at gmail.com
Fri Jun 14 10:01:15 CEST 2013
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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