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
ATOMS
the group of atoms that you are calculating the Gyration Tensor for.
=1,1,10 The CENTER action with label c1 calculates the following quantities:
Quantity
Description
c1.x
Glossary of keywords and components
Description of components
Quantity
Description
.#!value
the position of the center of mass
The atoms involved can be specified using
ATOMS
the group of atoms that you are calculating the Gyration Tensor for. For more information on how to specify lists of atoms see Groups and Virtual Atoms
Compulsory keywords
TYPE
( default=RADIUS ) The type of calculation relative to the Gyration Tensor you want to perform
Options
NOPBC
( default=off ) ignore the periodic boundary conditions when calculating distances
PHASES
( default=off ) use trigonometric phases when computing position of center
SAFE_PHASES
( default=off ) use trignomentric phases when computing position of center but also compute the center in ths usual way and use this when the pbc are not set. There are two reasons for using this option (1) you are doing something that you know is really weird or (2) you are an idiot
MASS
( default=off ) calculate the center of mass
WEIGHTS
what weights should be used when calculating the center. If this keyword is not present the geometric center is computed. If WEIGHTS=@Masses is used the center of mass is computed. If WEIGHTS=@charges the center of charge is computed. If the label of an action is provided PLUMED assumes that that action calculates a list of symmetry functions that can be used as weights. Lastly, an explicit list of numbers to use as weights can be provided
