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

[Johnny Lu]

Going from non-shift to shifted potential changes the energy. So I was not
surprised by the sudden jump of energy between step 0 and step 10 for the
previous simulation (npt14).

But the jump near step 0 for the current simulation (npt15) is not right.

This is an equilibration run.

I have just uploaded the files at http://redmine.gromacs.org/issues/1640


On Tue, Nov 11, 2014 at 10:54 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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