Re: coordNum colvar with dummyAtom

From: Giacomo Fiorin (
Date: Thu Dec 22 2011 - 17:41:20 CST

Hi Ernesto, that would not be a bug strictly speaking, but a lack of
support for a very peculiar configuration. In almost all cases, you would
want to compute the number of contacts between two groups of atoms.
Because in NAMD drifts due to residual center of mass motion cannot be
completely stopped to optimize parallel performance, coordNum does not
cover the case where one of the two groups is not made of real atoms, but
of a dummy atom fixed in space.

dummyAtom will help you instead if you want to keep a portion of the system
around a fixed position, which you can do also in your case, setting up a
distance variable between a group and that dummy atom. You can then
compute the coordination number, specifying the restrained group as group2
and using group2CenterOnly if you only want the number of atoms within a
certain region.

Restraining the distance between that group and the dummyAtom, thereby
stopping its drift, is also useful later when analyzing the trajectory.

On Dec 19, 2011 7:57 PM, "Ernesto Vargas" <> wrote:

> I am using the compiled binary for NAMD_2.8_Linux-x86_64-CUDA.
> When using the coordNum colvar, I notice that it always returns 0 if my
> group is defined by a dummyAtom.
> Is this a bug?

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:05 CST