Re: colvar: coordnum output

From: Jérôme Hénin (
Date: Fri Apr 30 2010 - 07:16:44 CDT

Dear Neelanjana,

On 30 April 2010 12:34, Neelanjana Sengupta <> 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


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