[gmx-users] RE: About the binary identical results by restarting from the checkpoint file

[Cuiying Jian]

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