From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
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
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_<at>_gmail.com
web: http://www.cmm.upenn.edu/
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On Mon, Feb 23, 2009 at 11:23 AM, Lisa Brown <lisa.brown2009_at_gmail.com> 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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