Re: fix atoms in minimisation

From: Leandro Martínez (leandromartinez98_at_gmail.com)
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
that
you protein environment becomes relaxed.
  Leandro.

------------------------------------
Leandro Martinez
Institute of Chemistry
State University of Campinas
http://www.ime.unicamp.br/~martinez/packmol
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On 5/1/06, Maria Gonzalez <mela_dn_at_yahoo.co.uk> 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.
>
> Send instant messages to your online friends http://uk.messenger.yahoo.com
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