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 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.

Note: As an experimental feature, CENTER also supports a keyword PHASES. This keyword finds the center of mass for sets of atoms that have been split by the period boundaries by computing scaled coordinates and average trigonometric functions, similarly to CENTER_OF_MULTICOLVAR. Notice that by construction this center position is not invariant with respect to rotations of the atoms at fixed cell lattice. In addition, for symmetric Bravais lattices, it is not invariant with respect to special symmetries. E.g., if you have an hexagonal cell, the center will not be invariant with respect to rotations of 120 degrees. On the other hand, it might make the treatment of PBC easier in difficult cases.

Examples

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

# 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 ATOMSthe list of atoms which are involved the virtual atom's definition. =1,1,10 The CENTER action with label c1 calculates the position of a virtual atom
# this is another way of stating the same:
c1bis: CENTER ATOMSthe list of atoms which are involved the virtual atom's definition. =1,10 WEIGHTSCenter is computed as a weighted average. =2,1 The CENTER action with label c1bis calculates the position of a virtual atom
# center of mass among these atoms:
c2: CENTER ATOMSthe list of atoms which are involved the virtual atom's definition. =2,3,4,5 MASS( default=off ) If set center is mass weighted  The CENTER 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.