Re: Colvars RMSD syntax with a moving reference frame

From: Giacomo Fiorin (
Date: Fri Aug 02 2013 - 13:17:49 CDT

Hello Christopher, to complete what Jrme was writing: up to and including
version 2.9, we had for RMSD a treatment of the rotational fit different
from other components, due to some minor implementation constraints related
to the calculation of system forces (e.g. ABF). In particular, RMSD's own
rotational fit code did not recognize refPositionsGroup.

We later merged the RMSD's own rotational fit code with that of the other
variable types, so that now they all share the same functionality,
including refPositionsGroup.

The way you wrote your configuration, it appears that you took as reference
the latest documentation, where RMSD has no particular restrictions. You
should also use the version of the code, that will soon become NAMD 2.10:
although the nightly builds don't include MacOSX, you can download the
latest source code and recompile, or update the NAMD 2.9 source code with
the script from


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