From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Sep 03 2006 - 08:10:10 CDT
VMD provides both the PMEPot
(http://www.ks.uiuc.edu/Research/vmd/plugins/pmepot/) and APBSRunba
(http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/) plugins to help
with electrostatics calculations. Of these, PMEPot is probably the one
you want to look at if you're interested in analyzing a trajectory from
NAMD; please see the paper referenced on the plugin page.
Neelanjana Sengupta wrote:
> Hi Ekta,
> Since the field is a vector, you'd calculate it on some atom (or
> defined point) in your systems, due to the other points. You basically
> write a script to calculate SUM(q/r^2). Keep the units in mind.
> I am doing this myself right now.
> On 9/2/06, *Ekta Khurana* <ekta_at_vitae.cmm.upenn.edu
> <mailto:ekta_at_vitae.cmm.upenn.edu>> wrote:
> Has someone tried to calculate the electric field in the system
> from a
> NAMD simulation?
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