From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Mar 20 2012 - 08:14:04 CDT
At this point a mass-weighted RMSD is not implemented, so the only
thing you could do is switch the translational restraint to COG. But
frankly, I don't expect this to make a noticeable difference.
Best,
Jerome
On 20 March 2012 02:47, <poker_at_physics.usyd.edu.au> wrote:
> 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 RMSD).
>
> 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 coordinate.
>
> Thanks,
> Poker.
>
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