[gmx-users] How to fix the atom positions?

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Nov 26 12:42:39 CET 2005

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.



On 11/26/05, Rahul Karyappa <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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