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

From: Margaret S. Cheung (mscheung_at_UH.EDU)
Date: Mon Mar 26 2007 - 08:49:42 CDT

Thank you very much for sharing the conf file!
Sincerely,
Margaret

Grzegorz Jezierski wrote:
> I've run simulations with almost any combination of Rotating Constraints,
> Harmonic Constraints, Fixed Atoms and PMF constraints. Here is a relevant
> part of one of my input files:
>
> Constraints on
> consRef R6G_6CAA.pdb
> consKFile fixed.pdb
> consKCol B
>
> rotConstraints on
> rotConsAxis 3.50 4.15 -20.45
> rotConsPivot 3.50 4.15 -24.37
> rotConsVel 0.0030
>
> freeEnergy on
> freeEnergyConfig pmf.conf
>
>
> Regards,
> Greg
>
>
> On Sun, 25 Mar 2007, 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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