to Tsjerk Wassenaar Sir Re: Re: [gmx-users] How to fix the atom positions?

[Rahul Karyappa]

Dear Sir,

   Thank you for your kind reply. If I want to fix the atom
positions still do I need to include angles, dihedrals in the topology
file? Waiting for your valuable kind reply.


Rahul Karyappa

-- Original Message --
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Sat, 26 Nov 2005 12:42:39 +0100
Subject: Re: [gmx-users] How to fix the atom positions?
Hi Rahul,
It
depends how fixed you want. You could make it a freeze group and it
will stay exactly where and the way it is. However, a better idea is to
use position restraints, which will attach each atom to a reference
with a spring constant. For this you have to add a [
position_restraints ] section in the topology file. I think it's
chapter 5 of the manual.
Cheers,
Tsjerk
On 11/26/05, Rahul Karyappa <<r.karyappa at ncl.res.in>r.karyappa at ncl.res.in> wrote:

Dear all,

   I want to fix the atom positions of one of my chain
structure. How can I do that? Do I need to make any changes in the
topology file or any other file? Please suggest me the way to do this.

Thanking you in advance.


Rahul Karyappa

NCL, Pune



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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336


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