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.
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.
Cheers,
Cuiying
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