From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Apr 14 2010 - 04:39:57 CDT
Dear Neelanjana,
I did send a bug advisory mentioning a problem with RMSD in ABF:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/10236.html
The message also stated that a fix would be made available shortly. It
was actually pushed to CVS back in June 2009 (see
http://www.ks.uiuc.edu/Research/namd/cvs2html/chronological.html).
So in principle, you should be able to run ABF with RMSD variables.
Actually we used it in some calculations in this paper:
http://pubs.acs.org/doi/abs/10.1021/ct9004432
Otherwise, running metadynamics is always an option.
Best,
Jerome
On 14 April 2010 07:54, Neelanjana Sengupta <senguptan_at_gmail.com> 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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