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

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 11 16:54:59 CET 2014

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


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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