VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Mar 10 2006 - 08:45:18 CST

Hi,

you can use the RMSDTT plugin:
http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/index.html

Best,

Luis

Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021

Tel: (212) 746-6375
Fax: (212) 746-8690
lug2002_at_med.cornell.edu

Richard Wood said the following on 03/09/06 22:20:
> Hi all,
>
> Is there a way to align all the frames of a dynamics calculation using
> VMD? I know that one can open two or more molecule files and do an
> alingment on them, but I need to know if I can do this with a dynamics
> trajectory having 100 frames or more. I need to align all the
> structures and then calculate RMSD's. Any help will be most appreciated.
>
> Richard
>
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> rwoodphd_at_yahoo.com
>
>
>