AMBER Archive (2006)Subject: Re: AMBER: the RMSD of MD
From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sun Sep 24 2006 - 12:49:52 CDT
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_at_qtp.ufl.edu
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