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 atoms should be in the proper periodic image. This is done automatically since PLUMED 2.2, by considering the ordered list of atoms and rebuilding the molecule using a procedure that is equivalent to that done in WHOLEMOLECULES . Notice that rebuilding is local to this action. This is different from WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.

In case you want to recover the old behavior you should use the NOPBC flag. In that case you need to take care that atoms are in the correct periodic image.

Examples

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:

Click on the labels of the actions for more information on what each action computes

c1: COM ATOMSthe list of atoms which are involved the virtual atom's definition. 
=1-7 The COM action with label c1 calculates the position of a virtual atom
c2: COM ATOMSthe list of atoms which are involved the virtual atom's definition. 
=15,20 The COM action with label c2 calculates the position of a virtual atom
d1: DISTANCE ATOMSthe pair of atom that we are calculating the distance between. 
=c1,c2 The DISTANCE action with label d1 calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. 
=d1 The PRINT action with label

Glossary of keywords and components

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

Options

NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
MASS	( default=off ) If set center is mass weighted
PHASES	( default=off ) Compute center using trigonometric phases
WEIGHTS	Center is computed as a weighted average.
SET_CHARGE	Set the charge of the virtual atom to a given value.
SET_MASS	Set the mass of the virtual atom to a given value.