colvar: coordnum output

From: Neelanjana Sengupta (
Date: Fri Apr 30 2010 - 05:34:29 CDT

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,

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