	This is part of the pamm module
	It is only available if you configure PLUMED with ./configure –enable-modules=pamm . 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 electronegative atoms are adjacent if they are hydrogen bonded

Examples

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	Keyword	Description
w	COMPONENTS	the weight of the connection
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

GROUP	the atoms for which you would like to calculate the adjacency matrix. For more information on how to specify lists of atoms see Groups and Virtual Atoms
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.

Or alternatively by using

GROUPC

. For more information on how to specify lists of atoms see Groups and Virtual 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
ORDER	( default=dah ) the order in which the groups are specified in the input. Can be dah (donor/acceptor/hydrogens), adh (acceptor/donor/hydrogens) or hda (hydrogens/donor/hydrogens
CLUSTERS	the name of the file that contains the definitions of all the kernels for PAMM
REGULARISE	( default=0.001 ) don't allow the denominator to be smaller then this value
GAUSS_CUTOFF	( default=6.25 ) the cutoff at which to stop evaluating the kernel function is set equal to sqrt(2x)(max(adc)+cov(adc))

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