GHOST

This is part of the vatom module

Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms.

The computed ghost atom is stored as a virtual atom that can be accessed in an atom list through the the label for the GHOST action that creates it.

Examples

The following input instructs plumed to print the distance between the ghost atom and the center of mass for atoms 15,20:

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

c1: GHOST 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=1,5,10 
COORDINATES
coordinates of the ghost atom in the local reference frame. 
=10.0,10.0,10.0 The GHOST action with label c1 calculates the position of a 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 position of a 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
the 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
COORDINATES	coordinates of the ghost atom in the local reference frame. For more information on how to specify lists of atoms see Groups and Virtual Atoms