This is part of the vatom module

Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. The computed ghost atom is stored as a virtual atom that can be accessed in an atom list through the the label for the GHOST action that creates it.

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
COORDINATES	coordinates of the ghost atom in the local reference frame. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Examples

The following input instructs plumed to print the distance between the ghost atom and the center of mass for atoms 15,20:

c1: GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0
c2: COM ATOMS=15,20
d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1