CONTACT_MATRIX

	This is part of the adjmat module
	It is only available if you configure PLUMED with ./configure –enable-modules=adjmat . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff.

As discussed in the section of the manual on Exploiting contact matrices a useful tool for developing complex collective variables is the notion of the so called adjacency matrix. An adjacency matrix is an \(N \times N\) matrix in which the \(i\)th, \(j\)th element tells you whether or not the \(i\)th and \(j\)th atoms/molecules from a set of \(N\) atoms/molecules are adjacent or not. These matrices can then be further analyzed using a number of other algorithms as is detailed in [107].

For this action the elements of the contact matrix are calculated using:

\[ a_{ij} = \sigma( |\mathbf{r}_{ij}| ) \]

where \(|\mathbf{r}_{ij}|\) is the magnitude of the vector connecting atoms \(i\) and \(j\) and where \(\sigma\) is a switchingfunction.

Examples

The input shown below calculates a \(6 \times 6\) matrix whose elements are equal to one if atom \(i\) and atom \(j\) are within 0.3 nm of each other and which is zero otherwise. The columns in this matrix are then summed so as to give the coordination number for each atom. The final quantity output in the colvar file is thus the average coordination number.

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

mat: CONTACT_MATRIX 
ATOMS
the atoms for which you would like to calculate the adjacency matrix. 
=1-6 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms.
={EXP D_0=0.2 R_0=0.1 D_MAX=0.66}   You cannot view the components that are calculated by each action for this input file. Sorry 
csums: COLUMNSUMS 
MATRIX
 could not find this keyword 
=mat 
MEAN
 could not find this keyword 
  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=csums.* 
FILE
the name of the file on which to output these quantities 
=colvar  You cannot view the components that are calculated by each action for this input file. Sorry 

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	a matrix containing the weights for the bonds between each pair of atoms

In addition the following quantities can be calculated by employing the keywords listed below

Quantity	Keyword	Description
w	COMPONENTS	a matrix containing the weights for the bonds between each pair of atoms
x	COMPONENTS	the projection of the bond on the x axis
y	COMPONENTS	the projection of the bond on the y axis
z	COMPONENTS	the projection of the bond on the z axis

The atoms involved can be specified using

GROUPA	. For more information on how to specify lists of atoms see Groups and Virtual Atoms
GROUPB	. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Or alternatively by using

ATOMS

the atoms for which you would like to calculate the adjacency matrix. This is a depracated syntax that is equivalent to GROUP. You are strongly recommened to use GROUP instead of ATOMS.

Compulsory keywords

NL_CUTOFF	( default=0.0 ) The cutoff for the neighbor list. A value of 0 means we are not using a neighbor list
NL_STRIDE	( default=1 ) The frequency with which we are updating the atoms in the neighbor list
NN	( default=6 ) The n parameter of the switching function
MM	( default=0 ) The m parameter of the switching function; 0 implies 2*NN
D_0	( default=0.0 ) The d_0 parameter of the switching function
R_0	The r_0 parameter of the switching function

Options

SERIAL	( default=off ) do the calculation in serial. Do not parallelize
COMPONENTS	( default=off ) also calculate the components of the vector connecting the atoms in the contact matrix
NOPBC	( default=off ) don't use pbc
GROUP	specifies the list of atoms that should be assumed indistinguishable. You can use multiple instances of this keyword i.e. GROUP1, GROUP2, GROUP3...
SWITCH	specify the switching function to use between two sets of indistinguishable atoms. You can use multiple instances of this keyword i.e. SWITCH1, SWITCH2, SWITCH3...