AMBER Archive (2008)

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

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Sat Jul 26 2008 - 11:09:38 CDT

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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