Re: colvar atom syntax

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Thu Jun 10 2010 - 15:15:41 CDT

I am having trouble finding an example colvarsConfig file. NAMD Some of the
Colvar documentation says that the format is similar to a regular NAMD
configuration file, but what parameters need to be set in it?

All I want is to restrict the internal motion of a subset of atoms in my
simulation. I do not want them fixed in space, but I want their relative
positions to remain roughly unchanged.

I do not have the colvarsConfig parameter set (no calvar config file) and
the simulation has not thrown any errors.

Mike

On Tue, Jun 8, 2010 at 1:11 PM, Michael Zimmermann <michaelz_at_iastate.edu>wrote:

> Dear NAMD users,
>
> I am having trouble finding the proper syntax for atom assignments within
> colvars. I want to keep a group of atoms that are in different segments
> constrained by RMSD to a reference position. This is what I have in my
> config file so far, but there seems to be something wrong...
>
> ================================
> colvars on
> colvar {
> rmsd {
> atoms {
> psfSegID P6
> atomNameResidueRange 231-235
> psfSegID P16
> atomNameResidueRange 232-235
> psfSegID P29
> atomNameResidueRange 232-235
> psfSegID P33
> atomNameResidueRange 25-28
> psfSegID P33
> }
> refPositionsFile markedProt.colvar.pdb
> refPositionsCol B
> }
> }
> ================================
>
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University
>

-- 
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

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