PROJECTION_ON_AXIS

This is part of the colvar module

Calculate a position based on the projection along and extension from a defined axis.

This variable takes 3 input atoms or pseudoatoms, using the two AXIS_ATOMS to define a linear vector. The position of the ATOM is then calculated relative to this vector, with two output components. The projection on the axis (proj) is the distance along the axis from the ATOM to the origin. The extension (ext) is the orthogonal distance between the ATOM and the axis.

Examples

This command tells plumed to define an axis, by calculating a vector that passes through atom 1 and atom 2. The position of atom 3 as a projection along this vector is calculated and printed to COLVAR1. At the same time, the perpendicular distance of atom 3 from the axis, the extension, is printed to COLVAR2.

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

poa: PROJECTION_ON_AXIS 
AXIS_ATOMS
The atoms that define the direction of the axis of interest. 
=1,2 
ATOM
The atom whose position we want to project on the axis of interest. 
=3 The PROJECTION_ON_AXIS action with label poa calculates the following quantities:

 Quantity   
 Description  
poa.proj
The value of the projection along the axis
poa.ext
The value of the extension from the axis


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=poa.proj 
FILE
the name of the file on which to output these quantities 
=COLVAR1 The PRINT action with label 
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=poa.ext 
FILE
the name of the file on which to output these quantities 
=COLVAR2 The PRINT action with label 

A particular application of this variable could be to study the motion of a ligand relative to its binding pocket on a protein. In this set of commands, the anchor points a1 and a2 are defined using example atom numbers within the protein. As a2 is attempting to be as close as possible to the center of the binding pocket, a COM is used when there are no suitable protein atoms. Similarly, a COM is used to define the position of the ligand in lig1. The calculated projection of lig1 along the axis defined between a1 and a2 is printed to COLVAR1. The calculated perpendicular extension of lig1 from the axis defined between a1 and a2 is printed to COLVAR2.

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

a1: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=3754 # Anchor point 1 The GROUP action with label a1 defines a group of atoms so that they can be referred to later in the input
a2: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=3019,4329,4744 # Anchor point 2 The COM action with label a2 calculates the position of a virtual atom
lig1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=5147-5190 # Ligand The COM action with label lig1 calculates the position of a virtual atom
pp: PROJECTION_ON_AXIS 
AXIS_ATOMS
The atoms that define the direction of the axis of interest. 
=a1,a2 
ATOM
The atom whose position we want to project on the axis of interest. 
=lig1 The PROJECTION_ON_AXIS action with label pp calculates the following quantities:

 Quantity   
 Description  
pp.proj
The value of the projection along the axis
pp.ext
The value of the extension from the axis


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=pp.proj 
FILE
the name of the file on which to output these quantities 
=COLVAR1 The PRINT action with label 
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=pp.ext 
FILE
the name of the file on which to output these quantities 
=COLVAR2 The PRINT action with label 

Glossary of keywords and components

The atoms involved can be specified using

AXIS_ATOMS	The atoms that define the direction of the axis of interest. For more information on how to specify lists of atoms see Groups and Virtual Atoms
ATOM	The atom whose position we want to project on the axis of interest. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances