OK. Thanks for the clarification.
James Kress Ph.D., President
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From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, August 04, 2021 7:16 AM
To: James Kress <jimkress_58.kressworks.org>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] SolvateOct box volume and cubic box information
That command is not obsolete. It will add the water and the box information. The box info is placed in the coordinate file. Dave just said that the box information in the prmtop file is not used.
On Wed, Aug 4, 2021, 12:31 AM James Kress <jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > wrote:
Are you saying that this command is wrong/ obsolete?
>> solvateOct protein TIP3PBOX 10
Jim
James Kress Ph.D., President
The KressWorksR Institute
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
"ENGINEERING THE CURE" C
(248) 573-5499
Learn More and Donate At:
Website: http://www.kressworks.org
Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
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original message.
-----Original Message-----
From: David A Case <dacase.chem.rutgers.edu <mailto:dacase.chem.rutgers.edu> >
Sent: Tuesday, August 03, 2021 9:08 PM
To: AMBER Mailing List <amber.ambermd.org <mailto: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 Wed Aug 04 2021 - 22:00:02 PDT
