Re: AMBER: frozen x unfrozen

From: David A. Case <>
Date: Wed, 22 Oct 2003 16:58:41 -0700

On Tue, Oct 21, 2003, Herbert Georg wrote:

> I would like to perform a simulation with a system in which one molecule
> has to be flexible and the other has to be frozen (at least the bonds
> have to be frozen). Is this possible??
> I was reading about the keyword NTR and the group section but it's not
> clear to me if the restraints are about the absolute positions of the
> specified atoms or if its about their bonds.

Ntr refers to the abosolute positions. I'm not sure what you mean when you
say one molecule has to be "frozen". You could use ntr=1 to keep one molecule
in a (nearly) fixed position and allow the other one to move.

...good luck...dac

> Can I apply SHAKE to the molecule I want to keep frozen only?

You can apply SHAKE to the part of the molecule that is also restrained by ntr

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Oct 23 2003 - 01:53:01 PDT
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