nan for Drude's LP in distance-like colvars

From: Bogdan MAREKHA (
Date: Fri Nov 24 2017 - 10:44:01 CST

Dear NAMD community,

I am running some /a posteriory/ analysis of my MD trajectories
generated with the latest CHARMM Drude polarizable force-field using the
capabilities of the collective variable module.

The problem I am facing is that whenever I call distance,distanceZ or
distanceVec colvar component involving at least one LP-type site I get a
/nan/ as an output. It also happens with other geometrical colvars like
angle or dihedral. Everything works fine for other types of Drude
interaction sites like D***. This has been tested with the NAMD 2.12
release version and with the latest night build (24.11.2017).

Does anybody have an idea of possible reasons for that?

Another interesting observation is that I do have access to the
coordinates of the LP-sites via cartesian colvar component. This means
that I can overcome those /nan/'s by constructing the corresponding
colvars using linear combinations, custom functions or scripted

distanceVec {

     group1 { atomNumbers 1 }

     group2 { atomNumbers 2 }


could be equivalently computed as

cartesian {

     componentCoeff -1.0

     atoms { atomNumbers 1}


cartesian {

     componentCoeff 1.0

     atoms { atomNumbers 2}



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