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

From: Grzegorz Jezierski (jezierski_at_theo1.theochem.tu-muenchen.de)
Date: Mon Mar 26 2007 - 04:46:53 CDT

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/
>
>

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