Action: GHOST

Module	vatom
Description	Usage
Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms.
This action outputs data to a file. You can read more about how PLUMED manages output files here

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

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

This action allows you to create a virtual atom that has a fixed set of coordinates in a local reference frame that is formed by three atoms. The way that this action is used is illustrated below:

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

c1The GHOST action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by GHOST action: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,5,10 COORDINATEScoordinates of the ghost atom in the local reference frame=10.0,10.0,10.0
c2The COM action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
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=15,20
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
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=c1,c2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1

Notice that ghost atom's position is stored as a virtual atom. The position of this atom can thus be used in the DISTANCE command by using the label for the GHOST action.

The position of the ghost atom c1 for the input above is:

$$r_{c1} = r_1 + 10\hat{a} + 10c + 10 \hat{b} 10\hat{c}$$

where unit vectors, $\hat{a}$, $\hat{b}$ and $\hat{c}$ in the expression above are obtained by dividing each of the three (orthogonal) vectors below by their magnitudes:

$$a = (r_5-r_1) \quad b = (r_5-r_1) \time (r_{10}-r_1) \quad (r_5-r_1)\times b$$

In all these expressions $r_i$ is used to indicate the position of atom $i$. If you run with periodic boundary conditions these are taken into account automatically when computing the differences between position vectors above. The way this is handled is akin to the way molecules are rebuilt in the WHOLEMOLECULES command. For the example above this would ensure that atom 5 is shifted to the periodic image where it is closest to atom 1 and atom 10 is shifted to the periodic image where it is closest to atom 10. If you wish to turn off this behaviour and you wish to disregard the periodic boundaries when computing these differences you should use the NOPBC flag.

Syntax

The following table describes the keywords and options that can be used with this action