From: Aaron Oakley (
Date: Sun Jan 08 2012 - 18:30:08 CST

Greetings all,

I'd like to perform an ILS calculation on a small protein
that undergoes significant rotation during a 6 ns simulation.
As I understand it, the tcl script produced by VMD corrects for
molecule translation but not rotation.

If I use the new collective variables facility in NAMD to prevent
rotation of the molecule, will this bias the calculation in an unacceptable