[gmx-users] restarting of shifted potential, 4.6.7 bug?

[Mark Abraham]

On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi.
>
> I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
> from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
> -4e5, which is fine.
>
> After that, I continue the 30ns NPT with the same mdp file, except with a
> longer run time (300ns).
>
> The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now at
> about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed after
> step 0?
>

IIRC, the restart ought to compute the same energy on the initial
coordinates as it did at the end of the previous run, and even if there's
no re-computation on the same coordinates, obviously it should not  jump by
1e5 in a few steps (or one? can't tell from the resolution). I would think
that might be a bug in filling a data structure for the output, but
probably not one in the simulation itself. Please file an issue at
http://redmine.gromacs.org, tarballing all the relevant files, and I'll try
to look at it.

The long-time behaviour of both simulations is pretty suspect though. Since
you're prepared to be ultra-conservative with your non-bonded and SETTLE
settings, I would explore using a 0.5fs time step (in normal and
ultra-conservative mode). Berendsen is not a good barostat algorithm for
production work, too... but I would not expect such a problem from its use.
Perhaps more importantly, why are you turning off the long-range dispersion
correction?

Mark

I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
> grompp for both simulations.
>
> The plot of total energies for the two simulations:
> http://oi60.tinypic.com/ddmejd.jpg
> The two mdp files: http://oi58.tinypic.com/11980si.jpg
>
> The commands that I used for continuing the simulations:
>
> The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp -f
> npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
>
> The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
> npt15.mdp -c npt14.tpr -t npt14_step30000000.cpt -o npt15.tpr
>
> Thanks.
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