VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 27 2009 - 13:18:17 CDT

On Tue, 2009-10-27 at 13:42 -0400, Bob Johnson wrote:
> Well...the trajectory is from a replica exchange simulation. Thus,
> there are
> discontinuities in the trajectory where the protein coordinates change
> rapidly. I have all the coordinates aligned the best I can (i.e. the
> center
> of each protein configuration is situated close to the origin), but
> the
> rapid jumps are still going to be there.

bob,

this error happens whenever stride fails. if i remember correctly,
it also fails when you have "unusual" hydrogen bonds. if you are
looking at the higher temperature replica, this could be an explanation.

cheers,
   axel.

>
> I'm not sure what you mean by "large magnitude atom coordinates".
> Thanks,
> Bob
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.