This is part of the vatom module

Calculate the center for a group of atoms, with arbitrary weights.

The computed center is stored as a virtual atom that can be accessed in an atom list through the label for the CENTER action that creates it. Notice that the generated virtual atom has charge equal to the sum of the charges and mass equal to the sum of the masses. If used with the MASS flag, then it provides a result identical to COM.

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

MASS

( default=off ) If set center is mass weighted

WEIGHTS

Center is computed as a weighted average.

Examples

# a point which is on the line connecting atoms 1 and 10, so that its distance
# from 10 is twice its distance from 1:
c1: CENTER ATOMS=1,1,10
# this is another way of stating the same:
c1bis: CENTER ATOMS=1,10 WEIGHTS=2,1

# center of mass among these atoms:
c2: CENTER ATOMS=2,3,4,5 MASS

d1: DISTANCE ATOMS=c1,c2

PRINT ARG=d1