Thanks a million Charles -- "fixupCovalentGeom" was the culprit. VdW
energies are now nice and negative, similar to results from refine_gentle.inp.
Thanks again (and please don't worry, the "ELEC" was just to help diagnose
what was going on; btw - when turned on, they are now nice and negative as
well), - Mark
On Tue, Oct 21, 2008 at 11:54:12AM -0400, Charles at Schwieters.org wrote:
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> Hello Mark--
>
> > Someone here wants to run a refinement along the lines of the old xplor
> > refine_gentle.inp (long rMD run, full VDW & electrostatics). Has anyone
> > done something like this using the python interface? Over the weekend,
> > tried
> > replacing initNBond() with things like:
>
> >
> > with "repel=0", VDW energies remain very high (+5000-8000) and
> > similarly ELEC values are ~ +1000.
>
> Is this a much different result than what you got with
> refine_gentle.inp? How are the resulting structures? Make absolutely
> certain that there are no calls to protocol.initNBond in this case. Be
> advised that running electrostatics without solvent is iffy.
>
> >
> > not setting "repel=0" gives low, but still postive values.
>
> For repel=0, VDW energies are always positive.
>
> >
> > Any ideas whether it's the parameter/topology set ('protein'),
>
> this shouldn't be the problem.
>
> > or
> > REPEL being assumed elsewhere in the python code,
>
> protocol.initNBond is called in fixupCovalentGeom- there's a
> possibility.
>
> > or -- most likely --
> > operator error at this end? We can certainly just use the old-xplor
> > refine scripts, but would like to move to python as much as possible,
> > so it seemed worth asking.
>
> I'm happy to investigate this further.
>
> best regards--
> Charles
