How to "twist" a molecule?

From: Margaret S. Cheung (mscheung_at_uh.edu)
Date: Thu Mar 22 2007 - 18:02:57 CDT

Hi NAMD users and developers,

I'd like to "twist" a molecule by applying a torque along an axis. I am
looking at "rotating constraints" in the user guide. But a simple
rotation is not what I want. Somehow I would want to "fix" a few distant
atoms away from the pivot point so that the molecules can be twisted
eventually (ex: like winding up a helical structure). If so, would you
recommend including "harmonic constraints" or simply assigning a few
"fixed" atoms to the reference pdb file in order to accomplish that?
Please advise and thank you for your time.

Sincerely,

-- 
Margaret S. Cheung
Assistant Professor
Department of Physics
629C Science and Research 1
University of Houston
Houston, TX 77204-5005
email:   mscheung_at_uh.edu
(O)713-743-8358 (F)713-743-3589
http://thoth.phys.uh.edu/~mscheung/

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