AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Jul 26 2008 - 12:20:11 CDT

I suggest comparing to amber itself. there is good reason to think the
vmd/namd energy is wrong unless you carefully set the scaling factors.
the defaults are NOT right for amber force fields.

On 7/26/08, Alessandro Nascimento <al.s.nascimento_at_gmail.com> wrote:
> Hi everyone,
>
> 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 ?
>
> Thanks a lot,
>
> --alessandro
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
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Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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