From: Jorgen Simonsen (
Date: Mon Jul 19 2010 - 22:52:59 CDT

Hi all,

I have performed a MD simulation of a peptide in explicit water and would
like to identify the lowest energy structure of it. I thought I could use
NAMDenergy in vmd but I do not understand it fully. Naively, I just remove
the water and select all but this gives me a positive energy which then I
presume is a total energy(Epot+Ekin) but could I get the potential energy of
the structures using NAMDenergy or any other tools within VMD?

Thanks in advance,