colvar atom syntax

From: Michael Zimmermann (
Date: Tue Jun 08 2010 - 13:11:29 CDT

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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