Module: vatom

Description	Usage
actions for calculating the positions of virtual atoms
Authors: The PLUMED core developers

Details

Sometimes, when calculating a colvar, you may not want to use the positions of a number of atoms directly. Instead you may wish to use the position of a virtual atom whose position is generated based on the positions of a collection of other atoms. For example you might want to use the center of mass of a group of atoms. This module contains actions that calculatie the positions of these virtual atoms from lists of input atoms.

To specify to a colvar that you want to use the position of a virtual atom to calculate a colvar rather than one of the atoms in your system you simply use the label for your virtual atom in place of the usual numerical index. Furthermore, virtual atoms and normal atoms can be mixed together in the input to colvars as shown below:

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

com1The COM action with label com1 calculates the following quantities: Quantity    Type    Description  
com1 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,10
dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,com1

If you don't want to calculate CVs from the virtual atom. That is to say you just want to monitor the position of a virtual atom (or any set of atoms) over the course of your trajectory you can do this using DUMPATOMS.

Actions

The following actions are part of this module

Name	Description	Tags
ARGS2VATOM	Create a virtual atom from the input scalars	VATOM
CENTER	Calculate the center for a group of atoms, with arbitrary weights.	VATOM
COM	Calculate the center of mass for a group of atoms.	VATOM
FIXEDATOM	Add a virtual atom in a fixed position.	VATOM
GHOST	Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms.	VATOM

Quantity	Type	Description
d	scalar	the DISTANCE between this pair of atoms