How to "twist" a molecule? (resubmit)

From: Margaret S. Cheung (mscheung_at_UH.EDU)
Date: Fri Mar 23 2007 - 11:05:16 CDT

(I apologize if you are reading this message again. The previous one
perhaps was
bounced because I haven't registered my current email address to NAMD-L,
as warned
by NAMD-L regulators)

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.

Margaret S. Cheung
Assistant Professor
Department of Physics
629C Science and Research 1
University of Houston
Houston, TX 77204-5005
(O)713-743-8358 (F)713-743-3589

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:29 CST