Re: harmonic restraint between two atoms

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon May 26 2008 - 11:34:27 CDT

Dear Esben,

On Mon, May 26, 2008 at 10:55:16AM +0200, Esben A. Gad wrote:
> to the NAMD-L list
>
> I would like to: Restrain atom A at a distance X relative to atom B, using
> a harmonic constraint of force-constant K during an MD run
>
> In the NAMD manual, it seems that only constraints relative to points in
> space is implemented.

What NAMD calls constraints are actually the restraints you are looking
for. They have this name for historical reasons.

Best,
Leo

> From reading this list, I should apparently be able
> to make this work using tclForces, but as I have no knowledge of tcl
> scripting, I would greatly appreciate it if anybody could supply a sample
> script or a work-around, as I assume other namd users must have wanted to
> apply this type of restraint before.
>
> Thank you in advance
>
> Esben A. Gad
> Graduate student, Protein Design
> Novozymes, Denmark
>

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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