VMD-L Mailing List
From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon Jul 19 2010 - 22:52:59 CDT
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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,
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