AMBER Archive (2006)

Subject: AMBER: Pressure in MD

From: Fenghui Fan (
Date: Mon Oct 02 2006 - 15:55:16 CDT

Dear all,

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

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