Re: how to do a MD of small part of a protein, using namd?

From: Giacomo Fiorin (
Date: Mon Feb 23 2009 - 11:53:43 CST

Dear Lisa, you can use the fixedAtoms keyword to fix the rest of the protein.

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
 fax: (+1)-215-573-6233
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 mail: giacomo.fiorin_<at>
---- ----

On Mon, Feb 23, 2009 at 11:23 AM, Lisa Brown <> wrote:
> Dear NAMD users,
> I am a new namd user. I want to do a simulation of a part of a
> protein (relatively big ) considering the other part of the system as
> rigid. (i.e. I want to consider whole protein but only a small part
> must be flexible.) Can namd allow to select only part of a protein
> for molecular dynamics using periodic boundary conditions?
> How can I do this with NAMD?
> All suggestions are welcome.
> Thank you for your attention and time.
> Liza B.

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