Action: PROJECTION_ON_AXIS

Module colvar
Description Usage
Calculate a position based on the projection along and extension from a defined axis. used in 0 tutorialsused in 2 eggs
output value type
the value of the projection along the axis scalar

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name Type Keyword Description
proj scalar COMPONENTS The value of the projection along the axis
ext scalar COMPONENTS The value of the extension from the axis

Input

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

Keyword Type Description
AXIS_ATOMS atoms The atoms that define the direction of the axis of interest
ATOM atoms The atom whose position we want to project on the axis of interest

Further details and examples

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

This variable takes 3 input atoms or pseudoatoms. It uses 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
tested on2.11
poa: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=1,2 ATOMThe atom whose position we want to project on the axis of interest=3
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=poa.proj FILEthe name of the file on which to output these quantities=COLVAR1
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=poa.ext FILEthe name of the file on which to output these quantities=COLVAR2

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
tested on2.11
a1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3754            # Anchor point 1
a2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3019,4329,4744    # Anchor point 2
lig1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5147-5190       # Ligand
pp: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=a1,a2 ATOMThe atom whose position we want to project on the axis of interest=lig1
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=pp.proj FILEthe name of the file on which to output these quantities=COLVAR1
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=pp.ext FILEthe name of the file on which to output these quantities=COLVAR2

Syntax

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

Keyword Type Default Description
AXIS_ATOMS input none The atoms that define the direction of the axis of interest
ATOM input none The atom whose position we want to project on the axis of interest
NUMERICAL_DERIVATIVES optional false calculate the derivatives for these quantities numerically
NOPBC optional false ignore the periodic boundary conditions when calculating distances