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This is part of the vatom module

Calculate the center of mass for a group of atoms.

The computed center of mass is stored as a virtual atom that can be accessed in an atom list through the label for the COM action that creates it.

For arbitrary weights (e.g. geometric center) see CENTER.

When running with periodic boundary conditions, the user should take care that the atoms in the COM group actually are in the proper periodic image. This is typically achieved using the WHOLEMOLECULES action before COM calculation.

The atoms involved can be specified using
ATOMS the list of atoms which are involved the virtual atom's definition. For more information on how to specify lists of atoms see Groups and Virtual Atoms

The following input instructs plumed to print the distance between the center of mass for atoms 1,2,3,4,5,6,7 and that for atoms 15,20:

COM ATOMS=1-7         LABEL=c1
COM ATOMS=15,20       LABEL=c2

(See also DISTANCE and PRINT).