From: Margaret S. Cheung (mscheung_at_UH.EDU)
Date: Mon Mar 26 2007 - 08:51:16 CDT
Thank you for the email. I will update the result from experimenting
with these parameters soon.
Sincerely,
Margaret
JC Gumbart wrote:
> 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: mscheung_at_uh.edu
>> (O)713-743-8358 (F)713-743-3589
>> http://thoth.phys.uh.edu/~mscheung/
>
>
-- 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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