[gmx-users] Compiling;Van der Waals: switch attractive term off
Alessandro at polymer.kth.se
Mon Jul 3 11:15:48 CEST 2006
My idea is to do as suggested by van der Vegt in 1996JChPh.105.8849V. The attractive part of the LJ is turn off to avoid monomers from sticking together.
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
From: gmx-users-bounces at gromacs.org on behalf of Berk Hess
Sent: Mon 7/3/2006 10:55 AM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term off
>From: "Alessandro Mattozzi" <Alessandro at polymer.kth.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term
>Date: Mon, 3 Jul 2006 10:40:18 +0200
>How should I do it? Is force.c used by grompp or mdrun? I want to know if I
>can run on shared resources (by just preprocessing with the edited version)
>or I do have to run it locally.
I think you did not answer to my question yet.
For coarse-grained polymer models one usually sets the LJ force
to zero after the minimum.
But I don't know what you want to do exactly, so maybe you really
want to turn of the 1/r^6 term.
I that case it seems a bit complicated to me to edit Gromacs source code.
For a simple polymer you just have a few LJ parameters,
so I guess it is easier to just set all C6 parameters to zero
in the force field file.
If you use sigma and epsilon entries, it is little work to change these to
C6/C12 values. The manual describes how to do this.
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