lone pair velocities

From: Gergely Gyimesi (gergely.gyimesi_at_ibmm.unibe.ch)
Date: Wed Sep 25 2013 - 11:27:48 CDT

Dear NAMD users,

I have recently set up a system utilizing the lone pair functionality of
NAMD to define virtual interaction sites in molecules (e.g. ring
centers, nothing to do with polarizable force-fields). I have set up
the PSF and input files accordingly, and NAMD runs, but it complains and
stops because lone pair atoms get infinite velocities ("Atom XX velocity
is inf...").

Digging into the source code I found that
Sequencer::reassignVelocities() generates infinite velocities for lone
pairs (no check for zero atom mass is done), which are fixed for water
models in HomePatch::rattle1() but not for other lone pairs.

Since I am rather new to NAMD, I was wondering if this was a bug I
found, or maybe lone pair support is not fully implemented (only for
water models), or maybe it's something else I'm overlooking. Patching
Sequencer::reassignVelocities() to generate zero velocity for zero mass
atoms solved the issue for me.

If someone would advise on this, I would be grateful. I did not want to
include PSF and input files here, but I can send them if requested.

Gergely Gyimesi

Gergely Gyimesi, PhD
Postdoctoral Research Fellow
Institute of Biochemistry and Molecular Medicine
University of Bern
Bühlstrasse 28
CH-3012 Bern     | phone: +41 (0)31 631 4739
Switzerland      | mailto:gergely.gyimesi_at_ibmm.unibe.ch

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