AMBER Archive (2009)

Subject: [AMBER] (no subject)

From: Lake, Thomas (
Date: Thu Feb 26 2009 - 10:19:53 CST


I am trying to plot the energy vs time of a peptide during a MD
simulation. Since I want the energy of the peptide without solvent, I
strip the water molecules using ptraj. I'm not sure how to then obtain
the energy. I'm wondering if I should input the mdcrd file into sander
using the imin=5 option?

Any help would be appreciated


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