VMD-L Mailing List

From: poker_at_physics.usyd.edu.au
Date: Tue Mar 11 2008 - 01:09:20 CDT

There's been an earlier thread (IIRC,) about interaction energy depending
on cutoff values used, but..

I'm writing to ask whether people have a version of namdenergy.tcl (or
another script,) to calculate full electrostatics for a trajectory file at
each frame in a trajectory. 

--
- What I have been doing so far is to set the cutoff at arbitrary large
values (say 5000 Angs., ), which gives a small difference of ~unit
kcal/mol for electrostatics. It's good enough, but really inelegant.
- There is a significant difference between cutoffs and full
electrostatics:
Cutoff(Angs.)   Electrostatic (kcal)
100             -239.163
140             -224.893
200             -215.19
5000            -204.5
Quick script    -205.38 (partially due to differences in accuracy constants
used?)
- We wish to compare energy calculations from NAMD simulation results with
its components, e.g. vacuum electrostatic potential, VdW, etc.
So, before making a customised version of the plug-in, I'm wondering if
this has been done already?
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