From: Richard Wood (
Date: Thu Mar 09 2006 - 21:20:45 CST

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 L. Wood, Ph. D.
Computational Chemist
Cockeysville, MD 21030