COM

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 PBCs with 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.

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

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:

c1: COM ATOMS=1-7
c2: COM ATOMS=15,20
d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1