AMBER Archive (2008)

Subject: Re: AMBER: interaction energies in Amber and VMD/NAMD

From: David A. Case (
Date: Sat Jul 26 2008 - 19:36:46 CDT

On Sat, Jul 26, 2008, Alessandro Nascimento wrote:
> I wrote a simple program to read some information in the prmtop file
> and compute nonbonded energies (ele+vdw) from a sander/pmemd
> trajectory and I am trying now to compare my first test results with
> the ones from the plugin NAMDEnergy in VMD. For electrostatic
> computation, they match perfectly. For vdw, however, seems like
> vmd/namd overestimates the energetic contribution. Does anyone has any
> experience on comparing results between amber and vmd/namd ?

I don't have experience, but as a guess: Amber by default includes a
correction for vdw interactions beyond the cutoff; NAMD might not inlcude
such a term. How different are the results?


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