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 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 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=1-7 The COM action with label c1 calculates the following quantities:

 Quantity   
 Description  
c1.x
the x coordinate of the virtual atom
c1.y
the y coordinate of the virtual atom
c1.z
the z coordinate of the virtual atom
c1.mass
the mass of the virtual atom
c1.charge
the charge of the virtual atom


c2: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=15,20 The COM action with label c2 calculates the following quantities:

 Quantity   
 Description  
c2.x
the x coordinate of the virtual atom
c2.y
the y coordinate of the virtual atom
c2.z
the z coordinate of the virtual atom
c2.mass
the mass of the virtual atom
c2.charge
the charge of the virtual atom


d1: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=c1,c2 The DISTANCE action with label d1 calculates a single scalar value
PRINT 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=d1 The PRINT action with label 

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
x	the x coordinate of the virtual atom
y	the y coordinate of the virtual atom
z	the z coordinate of the virtual atom
mass	the mass of the virtual atom
charge	the charge of the virtual atom

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.