Re: colvars: free energy change with rmsd

From: Jérôme Hénin (
Date: Wed Apr 14 2010 - 04:39:57 CDT

Dear Neelanjana,

I did send a bug advisory mentioning a problem with RMSD in ABF:
The message also stated that a fix would be made available shortly. It
was actually pushed to CVS back in June 2009 (see

So in principle, you should be able to run ABF with RMSD variables.
Actually we used it in some calculations in this paper:

Otherwise, running metadynamics is always an option.


On 14 April 2010 07:54, Neelanjana Sengupta <> wrote:
> Dear NAMD experts,
> I am using the collective variables (colvar) module to calculate the free
> energy change as a function of the rmsd of one structure w.r.t another
> (reference) structure. Since Adaptive Biasing Force calculations do not
> support rmsd, I am employing the Harmonic restraints method. However, unlike
> ABF, this method does not yield an output file where one can get the
> energies as a function of the colvar. Am I right here? If so, can I get some
> alternative suggestions for getting the free energy change as a function of
> rmsd?
> Thanks,
> Neelanjana

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