Atom numbering

From: Felipe Merino (
Date: Sat Jun 22 2013 - 05:34:53 CDT

Hi all,

I have a very simple question for which i have found mixed info in the
list. As far as i know NAMD uses a 1-based numbering system (for
tclForces or Colvars but not for extraBonds). However, i have been
having lately some rattle failures. When i take the index from NAMD and
i look at the corresponding "serial" in VMD it is a heavy atom. Only by
used a 0-based numbering i get an actual hydrogen atom. It concerns me
since all my tclForces calculations assume the 1-bases system.

Any feedback will be appreciated



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