AMBER: Extracting periodic box size deviation

From: CJ Dickson <>
Date: Thu, 06 Nov 2008 23:29:20 +0000

Hi all,

I have run an equilibrium simulation with periodic boundary conditions
at constant pressure (similar to part of section 5 of the first Amber
tutorial). As expected the volume of the periodic box changes as the
system equilibrates.

I now want to plot how the values of the box dimensions (i.e. x, y &
z) change with time as the volume of the periodic box changes. Is
this possible? Perhaps there is a ptraj command that extracts such

Thanks for any help,

Callum Dickson
University of Edinburgh
Chemical Physics Undergrad.

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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Received on Fri Dec 05 2008 - 11:09:03 PST
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