Re: colvar: coordnum output

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Apr 30 2010 - 09:25:14 CDT

Hi Neelanjana, the coordNum variable doesn't support ABF at this stage. The
code should have brought up the error, though: sorry if it didn't. What
version of NAMD were you using? If you need a free energy for this
variable, you could try metadynamics on the same variable.

The range between 0 and 2,500 is only mathematical, most physically relevant
configurations will be somewhere in between. Before setting your lower and
upper boundaries, you can either make a guess of what they will be, or use
the full range (0 and 2500).

What was the value of the variable in the colvars.traj file? If it was
always, or even sometimes higher than 8, a higher value should be used as
upper boundary. A lower boundary of 0 for coordNum is generally a sensible
thing, though.

Giacomo

---- ----
Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science
    Temple University
    1900 N 12 th Street, Philadelphia, PA 19122
mail: giacomo.fiorin_at_gmail.com
---- ----

On Fri, Apr 30, 2010 at 6:34 AM, 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.
>
> 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), *and each A(x_i) is 0*!
> Similar things are reported in the .grad and .count files.
>
> Can I get some help here? Here are the key parts of my input:
>
>
> lowerBoundary 2.0
> upperBoundary 8.0
>
> coordnum {
> group1 {
> atomsFile a30tog33.pdb
> atomsCol O
> atomsColValue 2.0
> }
> group2 {
> atomsFile v18toa21.pdb
> atomsCol O
> atomsColValue 2.0
> }
> cutoff 4.0
> expNumer 6
> expDenom 12
> group2CenterOnly off
> }
> }
> abf {
> colvars cnum
> fullSamples 100
> hideJacobian no
> outputFreq 100
> applyBias yes
> }
>
>
> Thanks and regards,
> Neelanjana
>

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