Re: rigid molecule

From: David Tanner (guacamoleo_at_gmail.com)
Date: Sun Mar 28 2010 - 19:25:37 CDT

I believe what you are looking for is "fixed atoms".
http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node26.html#SECTION00084300000000000000
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
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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?
Thanks.
Mark

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:51 CST