Re: vmd-l: Aligning structures

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Fri Mar 10 2006 - 10:19:43 CST

  Hi Richard,

VMD can align and compute RMSD over trajectories very easily. Have a look
at the last section of the VMD tutorial at:

http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html

Marcos

On Thu, 9 Mar 2006, Richard Wood wrote:

> 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
>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:18 CST