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 - 19:46:58 CDT

I don't think Alessandro used Amber for energies, and if it's a simple program
it probably is non-periodic. I think it's likely the 1-4 scaling factor for vdw.
one of them ( can't recall, Adrian may know) either ele or vdw has the
wrong 1-4 scaling in NAMD for amber ff.

On Sat, Jul 26, 2008 at 8:36 PM, David A. Case <case_at_scripps.edu> wrote:
> 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?
>
> ...dac
>
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-- 
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Carlos L. Simmerling, Ph.D.
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