Collective variable on COM instead of COG

Date: Mon Mar 19 2012 - 20:47:53 CDT

I spotted that the collective variables component RMSD specifically
contrains internal freedoms by aligning with the center-of-geometry of
the molecule.

In our simulations we're using a translational constraint on the
center-of-mass at the same time (effectively a 2D-free energy
calculation on translational separation and internal freedom through

Does the code allow the RMSD constraint to align to the COM cordinates
instead? Or, should we consider switching to COG in the translational
reaction coordinate to keep the two coordinates independent? It is
perhaps inconsequential if we used only the heavy atoms C,N,O s in the


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