VMD-L Mailing List
From: poker_at_physics.usyd.edu.au
Date: Tue Mar 11 2008 - 01:09:20 CDT
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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? ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
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