Hi, Mark,
I reduce the length of test runs to only 6 steps now. The binary identical
continuation still cannot be obtained. I use gmxcheck to compare the results
according to your suggestions and I find two reasons to cause different
trajectories.
One is a water molecule happening to span the Y-boundary of the simulation box.
In the undivided run, the molecule locates at the +Y direction while it occurs
at the �CY direction in the continuous run. The differences of Y-coordinates
are exactly the box length. Certainly, X and Z coordinates in the two runs are
indeed identical.
The other one is the velocities of many atoms being different in the fifth or
sixth digits. The case becomes more and more serious with time.
After I change the different initial gro files, the first phenomenon disappears
because no spanning-boundary water occurs. However, the second one is always
there no matter which Gromacs is used, the single-precision or the
double-precision. So, my question is how to obtain the binary identical
continuation.
regards,
Guang-Jun
> Date: Mon, 23 Feb 2009 14:37:06 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] About the binary identical continuation by
> restarting from the checkpoint file
>
> GuoGuangjun wrote:
> > Hi, All
> >
> >
> >
> > Before to perform long simulations, I think it is necessary to do
> > continuous runs. I make several tests
> >
> > to check the reliability of restart by using the checkpoint file. First,
> > I do a 6ps-long run, and then do it
> >
> > again by two parts, that is, the first half (3 ps) starts from the same
> > initial gro file, followed by its
> >
> > second half. Here are my operations:
> >
> >
> >
> > grompp -f 6ps1.mdp -c water.gro -p water.top -o 6ps1.tpr
> >
> > mpirun -np 4 mdrun -s 6ps1.tpr -o 6ps1.trr -x 6ps1.xtc -e 6ps1.edr -dlb no
> >
> >
> >
> > grompp -f 3ps.mdp -c water.gro -p water.top -o 3ps.tpr
> >
> > mpirun -np 4 mdrun -s 3ps.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr -dlb
> > no -cpo 3ps.cpt
> >
> >
> >
> > tpbconv -s 3ps.tpr -extend 3.0 -o 6ps2.tpr -cont
> >
> > mpirun -np 4 mdrun -s 6ps2.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr -dlb
> > no -cpi 3ps.cpt -append
> >
> >
> >
> > The log file tells me----“Restarting from checkpoint, appending to
> > previous log file.” However, when I
> >
> > check the binary files, such as 6ps1.trr and 6ps2.trr, the cmp command
> > tells me they are not identical.
>
> Use gmxcheck for this test. This will give you either confirmation that
> you're achieving your objective, or enough information to find out why not.
>
> > During these tests, I have turned off the gen_vel, optimize_fft, and
> > dynamic load balancing (dlb) according
> >
> > to Gromacs manual and previous posters. How to obtain the binary
> > identical continuation? My computational
> >
> > environments are Gromacs 4.0.3, lammpi 7.1.4, Redhat Linux, two AMD
> > Opteron CPUs with dual cores
> >
> > in each, 500 SPC water molecules, and the NPT ensemble.
>
> Your approach looks right to me.
>
> Mark
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