	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 connected topologically

The atoms involved can be specified using

NODES

The list of atoms for which you would like to calculate the contact matrix. The atoms involved must be specified as a list of labels of MultiColvar or labels of a MultiColvar functions actions. If you would just like to use the atomic positions you can use a DENSITY command to specify a group of atoms. Specifying your atomic positions using labels of other MultiColvar or MultiColvar functions commands is useful, however, as you can then exploit a much wider variety of functions of the contact matrix as described in Exploiting contact matrices. For more information on how to specify lists of atoms see Groups and Virtual Atoms

ATOMS

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

Compulsory keywords

DENSITY_THRESHOLD
SIGMA	the width of the function to be used for kernel density estimation
KERNEL	( default=gaussian ) the type of kernel function to be used

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) do the calculation in serial. Do not parallelize
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
HIGHMEM	( default=off ) use a more memory intensive version of this collective variable
SWITCH	This keyword is used if you want to employ an alternative to the continuous swiching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords. You can use multiple instances of this keyword i.e. SWITCH1, SWITCH2, SWITCH3...
RADIUS	You can use multiple instances of this keyword i.e. RADIUS1, RADIUS2, RADIUS3...
CYLINDER_SWITCH	a switching function on ( r_ij . r_ik - 1 )/r_ij You can use multiple instances of this keyword i.e. CYLINDER_SWITCH1, CYLINDER_SWITCH2, CYLINDER_SWITCH3...
BIN_SIZE	the size to use for the bins You can use multiple instances of this keyword i.e. BIN_SIZE1, BIN_SIZE2, BIN_SIZE3...

Examples