RE: Modification of equlibrated simulation box: OPTION 4

From: Bishop, Thomas C (
Date: Wed Oct 21 2009 - 18:57:48 CDT

Just to throw out another option ...
if it's only solvent and it has the correct properties
then why not trim it to the size you want by cutting away excess solvent?


From: on behalf of Axel Kohlmeyer
Sent: Wed 10/21/2009 9:00 AM
Cc: namd-l
Subject: Re: namd-l: Modification of equlibrated simulation box

On Wed, 2009-10-21 at 13:36 +0800, wrote:
> Dear all,
> I have an equlibrated simulation box with dimension (lx,ly,lz). I
> want to modify its dimension to (lx',ly',lz'), where ly'>ly, lz'>lz
> and lx'<lx. Is there any proper method? I would be grateful if any of
> you could give me some advice.

there certainly is no method that would work without having
to reequilibrate the system.

if the change in the box lengths are not to drastic, i would
just rescale all x-, y-, and z-coordinates accordingly, reset
the box and then start the equilibration process again. note,
that such a "squeeze/stretch" will induce low level sound waves
traveling through your system, that will go on for a very long
time, unless you take precautions by repeatedly freezing different
parts of your system and relaxing the rest.

the second best option would be to remove the solvent and
resolvate according to your desired dimension.

the third option would be to apply external pressure until
the system has the shape that you want.


> 2009-10-21
> ______________________________________________________________________

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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