Re: rigid molecule

From: David Tanner (
Date: Sun Mar 28 2010 - 19:25:37 CDT

I believe what you are looking for is "fixed atoms".
I believe the above link will take you to the fixed atoms parameters
section of the online user's guide.

David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801

On Mar 28, 2010, at 3:34 PM, Mark M Huntress wrote:

Hi, I would like to simulate the reorientation of a molecule inside a
protein cavity, while keeping the molecule completely rigid- bonds,
angles and dihedrals. It should only be free to translate and rotate.
I tried rigidbonds all but that did not work, because it was still too
flexible to move (the dihedrals). Does anyone know if there is a way
to do this in NAMD?

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