From: Axel Kohlmeyer (
Date: Wed Apr 04 2018 - 05:04:34 CDT

On Wed, Apr 4, 2018 at 3:40 AM, Jeams Anderson <> wrote:
> Dear All
> I am wondering that, the RDF tools of VMD is able to calculate center of
> mass molecules or not.

it is not. if it would be, it would be mentioned in the user's guide.

> For instance If I have a hetero atom donated benzene
> like structure and all position have different partial charge, thus type of
> atoms are different six types. Now, If I select all six types in the
> selection 1 and for selection 2 consider one ion which is different type. In
> that case, for selection 1 it will consider center of mass of the six atoms?

no, it will compute the g(r) contribution from each atom and average over it.

> Further, from the first neighboring distance value if we can calculate the
> number of neighbor atoms then it should be considered as coordination
> number. Is it possible to calculate this parameter frame by frame in VMD?

g(r) and coordination numbers are well defined entities only for point
for anything more complex, you will have to devise a meaningful
algorithm and then implement it as a custom code.


> Further comments will be very helpful
> Thanks in advance
> With best regard
> Jeams

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.