Re: Colvars RMSD syntax with a moving reference frame

From: Mayne, Christopher G (
Date: Fri Aug 02 2013 - 16:38:21 CDT


Thanks Jerome and Giacomo for the advice. I compiled the latest nightly build of NAMD and re-ran the simulation as described--the resulting RMSD output matched my manual analysis. Issue resolved!

Christopher Mayne

On Aug 2, 2013, at 1:17 PM, Giacomo Fiorin wrote:

Hello Christopher, to complete what Jérôme 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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