From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Fri Apr 30 2010 - 07:32:55 CDT
Dear Jérôme,
Thanks for the pointers. I wanted to bring to your notice that I am using
NAMD2.7b2, and the run did continue without any errors:
colvars: Finished ABF setup.
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
Do you recommend metadynamics for coordnum calculations?
-Neelanjana
On Fri, Apr 30, 2010 at 5:46 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> Dear Neelanjana,
>
> On 30 April 2010 12:34, Neelanjana Sengupta <senguptan_at_gmail.com> wrote:
> > Dear NAMD experts,
> >
> > I am trying to calculate the free energy change between 2 atom groups
> (~50
> > atoms each) as a function of their coordination number (C), using the
> colvar
> > module with adaptive biasing force.
>
> This is a problem. At this point coordination number variables do not
> support ABF calculations. In principle, this should have triggered an
> error at startup. What version of NAMD are you using?
>
>
> > According to the manual, one should get the free energies as a fn. of C
> > (which should go from ~0 to ~2500 for me). However, my .pmf gives x_i in
> the
> > range from 0 to 8 (my lower and upper boundaries),
>
> Several points here:
>
> 1) output files such as .pmf and .count will only cover the range
> given by user-set boundaries
>
> 2) the theoretical limit of coordNum, in your case 2500, is to be
> taken with a grain of salt. You will only get to that value if all
> atoms in one group coordinate to all atoms in the other. In practice,
> because of saturation and steric constraints, such high values will
> not be sampled
>
> 3) the first place to go to understand the behavior of your colvars is
> the covlars.traj file
>
> Cheers,
> Jerome
>
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