From: Jeams Anderson (
Date: Wed Apr 04 2018 - 02:40:42 CDT

Dear All

I am wondering that, the RDF tools of VMD is able to calculate center of
mass molecules or not. 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?

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?

Further comments will be very helpful

Thanks in advance

With best regard