Re: colvar atom syntax

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Tue Jun 08 2010 - 15:01:41 CDT

Hi Michael, what NAMD version are you using and what is the error message?

"colvars on" is an option in the NAMD configuration file. It should be
followed by "colvarsConfig xxxx", much like "tclForces on" and
"tclForcesScript xxxx".

If you're using NAMD 2.7b2, specifying multiple psfSegID should work,
although I believe you have one too many.

Giacomo

---- ----
 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
 giacomo.fiorin_at_temple.edu
---- ----

On Tue, Jun 8, 2010 at 2:11 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
>

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