[gmx-users] RE: About the binary identical results by restarting from the checkpoint file
cuiying_jian at hotmail.com
Mon Jun 3 18:59:31 CEST 2013
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
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.
> 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
> 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 ;-)
More information about the gromacs.org_gmx-users