AMBER Archive (2006)

Subject: Re: AMBER: Pressure in MD

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon Oct 02 2006 - 16:24:30 CDT

Dear Fenghui,

this is a known effect and stemms from the low compressibility of liquids,
that accurately translates into huge changes of pressure with minimal
changes of volume/density. It is more informative to check the change in
system density and the average pressure of the run, for which I would
consider a value of ca. 1.0 with a standard deviation of 80 to be typical.

So, if everything else in your run looks ok, there should be no problem.

> During a constant pressure (300 K) productuve MD with
> periodic boundaries, I find the system pressure change
> significantly, from -70 to 200. I think this should
> significantly influence the conformation of the
> structure, leading to the fact the trajectory file
> will be significantly different from the structure in
> the native cell. In the living cell, we can consider
> the pressure as constant. Does the the pressure change
> in the MD process significantly influence the usage of
> our MD results to explain the biomolecular function?
>
> I am looking forward to getting your message.
>
> Best regards.
>
> Fenghui Fan

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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