Re: Atom numbering

From: Giacomo Fiorin (
Date: Sat Jun 22 2013 - 10:41:35 CDT

Hello Felipe, 0-based numbering are used internally by NAMD everywhere.
The convention used by tclForces and colvars is to use 1-based numbers as
input because they match the PSF and PDB, but once entered in the code they
are also decreased by 1 and become 0-based.

Unfortunately the rattle error message can be confusing because it prints
the 0-based internal number without converting it to a 1-based "external"

On Jun 22, 2013 6:36 AM, "Felipe Merino" <>

> 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
> best
> Felipe

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:22 CST