Take a look at gmx traj tool

https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-traj.html

with the flag -com you will get the center of mass of the selected group. It most likely won't fall on top of another atom anyway, but you can look for the nearest one, if needed.

Best

Nicola

PyMol:

https://pymolwiki.org/index.php/Center_of_mass

use centerofmass command in pymol

How about calculating that in Materials Studio?

I tried the perl script below:

#!perl

use strict;

use Getopt::Long;

use MaterialsScript qw(:all);

# Open the document

my $doc = Documents->Import("D:/Z/POO_Files/Documents/POP/629815-QESJAA-cek.xsd");

my $molecule = $doc->Molecule;

my $center = $molecule->CenterOfMass;

printf("CenterOfMass is: %.3f, %.3f, %.3f (Å)\n", $center->X, $center->Y, $center->Z);

However, after debugging, it says:

There are no objects in the "Molecules" collection (function/property "Molecule")

Well, I confirm that there is a molecule inside.

https://www.youtube.com/watch?v=vEMj80ft6TU