Re: AMBER: the RMSD of MD

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Sun, 24 Sep 2006 13:49:52 -0400

Fenghui Fan wrote:
> Dear all,
>
> When I run a productive MD, the RMSD value in the RMSD
> vs time curve gradually increases with the elongation
> time, but it cannot reach plateau. For this reason, it
> seems I cannot get a reasonable stble structure. Does
> anyone can give us a explaination on this?
>
> I am looking forward to ggetting your reply.
>
> Best regards.
>
> Fenghui Fan
>

we would need MANY more details such as how long did you run, what
solvent, what thermostat, how big is your system. More importantly
perhaps, are you positive that the system IS stable ?


> 


-- 
                            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 Sep 27 2006 - 06:07:06 PDT
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