VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 04 2018 - 05:04:34 CDT

On Wed, Apr 4, 2018 at 3:40 AM, Jeams Anderson <anddersonnyc_at_gmail.com> 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
particles.
for anything more complex, you will have to devise a meaningful
algorithm and then implement it as a custom code.

axel.

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

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.