AMBER Archive (2004)

Subject: Thanks - Re: AMBER: MD & running time

From: bybaker_at_itsa.ucsf.edu
Date: Tue Jun 22 2004 - 18:29:09 CDT

('binary' encoding is not supported, stored as-is) Hello, Linda:

Thanks for your advices !

Regards

Bo Yang

On Tue, 22 Jun 2004 15:12:00 -0400 (EDT) "Linda Prengaman" wrote:

> I'm not sure what your computational system for running MD is like, but in
> general I would say yes, so long a running time is to be expected.
> Reducing the size of the periodic box may help, as well as reducing the
> cutoff. However, reducing these may affect the accuracy of your
> simulation. You could cut down the number of steps you are running the
> system for, depending on how long it takes your system to stablize itself
> (Etot should hover around the same value). I'm not sure I can offer any
> advice about the confirmational changes your system is going through, but
> you might want to double check everything. Good luck.
> Linda Prengaman

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