Re: How to "twist" a molecule? (resubmit)

From: JC Gumbart (
Date: Sun Mar 25 2007 - 00:33:00 CDT

Your suggestion definitely sounds like it might work (using
fixedAtoms that is); you can't use harmonic constraints and rotating
constraints at the same time though, if I understand the manual
correctly. I haven't seen rotatingConstraints used by anyone myself,
so you may just need to experiment with it. You could also try using
IMD to control the forces interactively. Let us know how it goes.

On Mar 23, 2007, at 11:05 AM, Margaret S. Cheung wrote:

> (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
> email:
> (O)713-743-8358 (F)713-743-3589

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