About ref frame for rmsd vs time

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Jan 30 2008 - 00:52:48 CST

I am looking for a general discussion about the relative scope of different
reference frame in calculating rmsd vs time (frame 0, last frame, average, min
energy, etc). For example, I am experiencing that for the ligand either "Ref
frame 0" or "Ref last frame" give substantially the same rmsd/time plot, while
for the protein they differ very substantially.
Thanks
francesco pietra

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