analyzing NAMD trajectory with NAMD Energy

From: Markus Dahlgren (
Date: Mon Jul 29 2013 - 10:13:42 CDT


Does a NAMD trajectory need to be wrapped/unwrapped prior to evaluation
using NAMD Energy? I get different energies depending on whether the
trajectory has been unwrapped prior to using NAMD Energy. Visually I can
see that parts of the protein-ligand complex has crossed the boundary
border and appears on the other side of the water box. Does the NAMD
trajectory have only the central image coordinates? Is wrapping not
necessary for NAMD Energy trajectory analysis when inputting NAMD
trajectories? I have been using NAMD


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