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From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 05 2010 - 08:53:18 CDT

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2010/8/5 <politr_at_huji.ac.il>:
> Dear VMD users,
> I'm using NAMD energy plugin to calculate energy between peptide and water.
> In order to test the work of the plugin I started from putting "all" under
> selection and I loaded XSC file, parameter file and choose PME (like in
> simulation) . The problem is that the energies I'm getting are slightly
> different from the energies in the log file from the simulation itself. Does
> anyone have any idea what is the reason for the discrepancy?

- limited accuracy of the numbers in the .xsc vs. the internally stored
  numbers. similarly coordinates in .dcd file are truncated to single
  precision on writing
- different ordering of summation of energies.

cheers,
     axel
> Regina
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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