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

From: David A Case <>
Date: Tue, 3 Aug 2021 21:08:14 -0400

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

>> solvateOct protein TIP3PBOX 10
> 1.09471219E+02 *6.31036082E+01 6.31036082E+01 6.31036082E+01*

Two points here:

First: since the box size (often) changes during a simulation, it should
never have been put into the prmtop file -- the prmtop file is for things
that don't change. So, the information in the prmtop file is ignored: box
information is always taken from the coordinate file. (The information is
still there for backwards compatibility with *very* old files.)

(Second: however, the 109.47 value above did originally indicate that this
was a truncated octahedron, and not a cubic box.)

>* Box X = 63.104 Box Y = 63.104 Box Z = 63.104*
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471

Above is the box information taken from the input coordinate file.

>This means that box information saved in the topology file is used for the
>subsequent/production run.

This is not correct. As noted above, any box information in the prmtop file
is ignored.

...hope this helps....dac

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Received on Tue Aug 03 2021 - 18:30:02 PDT
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