Are you saying that this command is wrong/ obsolete?
>> solvateOct protein TIP3PBOX 10
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-----Original Message-----
From: David A Case <dacase.chem.rutgers.edu>
Sent: Tuesday, August 03, 2021 9:08 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] SolvateOct box volume and cubic box information
On Wed, Aug 04, 2021, Umesh Roy wrote:
>> solvateOct protein TIP3PBOX 10
>
>%FLAG BOX_DIMENSIONS
>%FORMAT(5E16.8)
> 1.09471219E+02 *6.31036082E+01 6.31036082E+01 6.31036082E+01*
>%FLAG RADIUS_SET
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 - 22:00:03 PDT
