Action: HBOND_MATRIX

Module adjmat
Description Usage
Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them. used in 1 tutorialsused in 0 eggs
output value type
a matrix containing the weights for the bonds between each pair of atoms matrix

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
w matrix COMPONENTS a matrix containing the weights for the bonds between each pair of atoms
x matrix COMPONENTS the projection of the bond on the x axis
y matrix COMPONENTS the projection of the bond on the y axis
z matrix COMPONENTS the projection of the bond on the z 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
GROUP atoms the atoms for which you would like to calculate the adjacency matrix
GROUPA atoms when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB atoms when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
ATOMS atoms the atoms for which you would like to calculate the adjacency matrix
DONORS atoms The list of atoms which can donate a hydrogen bond
ACCEPTORS atoms The list of atoms which can accept a hydrogen bond
HYDROGENS atoms The list of atoms that can form the bridge between the two interesting parts of the structure

Further details and examples

Text from manual goes here

References

More information about how this action can be used is available in the following articles:

Syntax

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

Keyword Type Default Description
GROUP input none the atoms for which you would like to calculate the adjacency matrix
GROUPA input none when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB input none when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
ATOMS input none the atoms for which you would like to calculate the adjacency matrix
DONORS input none The list of atoms which can donate a hydrogen bond
ACCEPTORS input none The list of atoms which can accept a hydrogen bond
HYDROGENS input none The list of atoms that can form the bridge between the two interesting parts of the structure
NL_CUTOFF compulsory 0.0 The cutoff for the neighbor list
NL_STRIDE compulsory 1 The frequency with which we are updating the atoms in the neighbor list
SERIAL optional false do the calculation in serial
COMPONENTS optional false also calculate the components of the vectors connecting the atoms in the contact matrix
NOPBC optional false don’t use pbc
SWITCH optional not used The switchingfunction that specifies how close a pair of atoms must be together for there to be a hydrogen bond between them. Options for this keyword are explained in the documentation for LESS_THAN.
HSWITCH optional not used The switchingfunction that specifies how close the hydrogen must be to the donor atom of the hydrogen bond for it to be considered a hydrogen bond. Options for this keyword are explained in the documentation for LESS_THAN.
ASWITCH optional not used A switchingfunction that is used to specify what the angle between the vector connecting the donor atom to the acceptor atom and the vector connecting the donor atom to the hydrogen must be in order for it considered to be a hydrogen bond. Options for this keyword are explained in the documentation for LESS_THAN.