CENTER

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:CENTERATOMS=1,1,10 # this is another way of stating the same:the list of atoms which are involved the virtual atom's definition.c1bis:CENTERATOMS=1,10the list of atoms which are involved the virtual atom's definition.WEIGHTS=2,1 # center of mass among these atoms:Center is computed as a weighted average.c2:CENTERATOMS=2,3,4,5the list of atoms which are involved the virtual atom's definition.MASS( default=off ) If set center is mass weightedd1:DISTANCEATOMS=the pair of atom that we are calculating the distance between.c1,c2

- Glossary of keywords and components

- Description of components

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. |