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

From: Margaret S. Cheung (mscheung_at_UH.EDU)
Date: Mon Mar 26 2007 - 14:09:33 CDT

Hello,

I tried with both rotational and harmonic contraints, but now I see the
possible problem JC mentioned.

The question is "how to set reference positions for rotating
constraints"? The manual simply said that the rotational constraints
parameters are specified in the same manner as for usual
(static)harmonic constraints". I assume it means that we need to set
consref, conskfile, conskcol for the harmonic constraints.

But if I now included rotational constraints to harmonic one, how can I
set the reference positions for rotation since all it has is
rotConsAxis, rotConsPivot and rotConsVel?
When I set constraints on, did it mean "all atoms" in the system will be
rotated? Can I apply rotation (twist) to only a part of the molecules
(e.g. excluding water molecules)?
Thank you.
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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