From: Stefan Franzen (
Date: Mon May 03 2010 - 08:48:10 CDT

I have tried to apply the directions provided in the User Guide to use
colvar. I am using the ubiquitin tutorial as a starting point. In fact,
you might say I am developing a tutorial section for colvar, which I would
be happy to make available (once I figure it out). I am quite frustrated
trying to apply the instructions. the "distance" works fine. But, the next
step for me of RSMD does not work no matter what I do. Here are two things
that I have tried. I have included my working file, which just tracks the
distance between the ends of ubiquitin as an example.

# option 1: put in the atom numbers #

colvar {
   rmsd {
      atoms { 1 2 3 }
      refPositionsFile ubq_ws.pdb

# option 2: put in the C-alphas #

myatoms {
  # add all the C-alphas within residues 1 to 76 of segment "U"
  psfSegID U
  atomNameResidueRange CA 1-76

colvar {
   rmsd {
      atoms { myatoms }
      refPositionsFile ubq_ws.pdb

Thank you,

Stefan Franzen
Professor of Chemistry
North Carolina State University
Raleigh, NC 27695
Phone: 919-515-8915