From: John Stone (
Date: Mon Feb 27 2006 - 16:06:56 CST

  VMD doesn't do any PB calculations internally, but we include a plugin
that helps setup and run APBS jobs from molecules loaded in VMD.

Also, there's a PME potential plugin that may be of interest if you
want to know what potentials NAMD is using for periodic simulations
using PME:

  John Stone

On Mon, Feb 27, 2006 at 01:19:48PM -0500, ivana adamovic wrote:
> Hello,
> I am quite new in using VMD, so I hope that this question was not answered
> already, if so, please just point me to where the solution of the problem
> was already described.
> I would appreciate help on how to obtain electrostatic potential map using
> VMD. Can it run PB calculations or we need to read in files form some of the
> MD codes?
> What is done in APBS Electrostatic part of the Analysis section and in PME ?
> Could you explain me a set up for both of these parts?
> Thanks a lot,
> Ivana Adamovic

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