From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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" <felipe.merino_at_mpi-muenster.mpg.de>
> 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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