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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
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