Re: harmonic restraint between two atoms

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon May 26 2008 - 12:01:15 CDT

On Mon, May 26, 2008 at 11:34:27AM -0500, Leonardo Trabuco wrote:
> 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.

I'm sorry, I misread your question. You can indeed do what you want with
TclForces. You can also accomplish this with the new extraBonds feature,
available in the CVS version of NAMD. To use this feature, add to your
config file:

extraBonds yes
extraBondsFile extrabonds.txt

In extrabonds.txt, add the line:

bond [atomid1] [atomid2] [k] [ref]

where atomid1 and atomid2 are the 0-based atom indices (note that NAMD
generally follows the 1-based scheme, so this can be confusing), k is
your force constant (in reality it is k/2, and given in kcal/mol/A^2),
and ref is your bond distance in Angstroms.

Sorry for the confusion.

Leo

>
> 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
>

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:30 CST