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

From: Lisa Brown (
Date: Mon Feb 23 2009 - 10:23:43 CST

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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