Re: fix atoms in minimisation

From: Leandro Martínez (
Date: Mon May 01 2006 - 15:20:56 CDT

You can use the "fixed atoms" option of NAMD. Set the fixed
atoms as all the protein atoms and the minimization will
not change their coordinates. As a next step you can equilibrate the
water and the membrane also keeping the protein atoms fixed in order
you protein environment becomes relaxed.

Leandro Martinez
Institute of Chemistry
State University of Campinas

On 5/1/06, Maria Gonzalez <> wrote:
> I have a set of 'unstable' protein structures that
> I have inserted in a lipid membrane. I would like to
> run a minimisation so that the lipids and water
> wrap the proteins, but conserving the initial geometry
> of the protein structure intact.
> The question is, is there a way to run a minimisation
> on only a set of atoms? In my case, the lipids and
> water.
> Thanks.
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