Re: [AMBER] SolvateOct box volume and cubic box information

From: David A Case <>
Date: Wed, 4 Aug 2021 08:09:44 -0400

On Wed, Aug 04, 2021, Umesh Roy wrote:

>Thank you very much for your reply. Yes, the box size may change during
>simulation. Maybe I should have placed my query in a better way. More
>precisely, I would like to know how the box dimension (Box X, Box Y, and
>Box z) is related to the volume of the truncated octahedron. Since the
>values of the box dimension are saved at a certain interval (at which we
>save our trajectories) during MD run in the coordinate file. How can I
>relate the volume of the truncated octahedron to the box dimension at a
>particular step?

One presentation of the formula is here:

The final line of a (formatted) coordinate file gives a,b,c,alpha,beta,gamma.
For a truncated octahedron, there is a single cell length and an single
angle, so you could simplify the formula some.

If you are doing constant pressure simulations (so that the unit cell volume
is changing), the volume is printed out along with the energies in the mdout


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Received on Wed Aug 04 2021 - 05:30:02 PDT
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