AMBER Archive (2008)

Subject: Re: AMBER: Extracting periodic box size deviation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Nov 06 2008 - 19:42:35 CST

> 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
> information?

You may be able to get the box via something like

% awk 'NF == 6 {print $1,$2,$3}' mdcrd > boxcrd

assuming box info is 3 lengths followed by 3 angles and the modulus of your
atom count does not leave a line with 6 numbers on it before the box.

% tail mdcrd

to see what you have.

Bill
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