Re: AMBER: Unstable RMS trajectory

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Tue, 17 Oct 2006 12:46:48 -0400

Did you rms fit the trajectory before attemping to compute the rms ?
otherwise you are looking at an rmsd going up simply because of difusion.

Also: are you sure you are computing rmsd for JUST the protein and NOT
the water atoms ? 



-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Wed Oct 18 2006 - 06:07:29 PDT
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