	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.

Print out the diameter of one of the connected components

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. When analyzing these matrix we can treat them as a graph and find connected components using some clustering algorithm. This action is used in tandem with this form of analysis to output the largest of the distances between the pairs of atoms that are connected together in a particular connected component. It is important to note that the quantity that is output by this action cannot be differentiated. As such it cannot be used as a collective variable in a biased simulation.

Examples

The following input uses PLUMED to calculate a adjacency matrix that connects a pair of atoms if they both have a coordination number that is greater than 2.0 and if they are within 6.0 nm of each other. Depth first search clustering is used to find the connected components in this matrix. The distance between every pair of atoms that are within the largest of the clusters found is then calculated and the largest of these distances is output to a file named colvar.

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

# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIESthis keyword is used for colvars such as coordination number. =1-512 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}  The COORDINATIONNUMBER action with label c1
# Select coordination numbers that are more than 2.0
cf: MFILTER_MORE DATAcompulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in =c1 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={RATIONAL D_0=2.0 R_0=0.1}  LOWMEM( default=off ) lower the memory requirements  The MFILTER_MORE action with label cf
# Build a contact matrix
mat: CONTACT_MATRIX ATOMSThe list of atoms for which you would like to calculate the contact matrix. =cf SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}  The CONTACT_MATRIX action with label mat
# Find largest cluster
dfs: DFSCLUSTERING MATRIXcompulsory keyword 
the action that calculates the adjacency matrix vessel we would like to analyze =mat The DFSCLUSTERING action with label dfs
clust1: CLUSTER_PROPERTIES CLUSTERScompulsory keyword 
the label of the action that does the clustering =dfs CLUSTERcompulsory keyword ( default=1 )
which cluster would you like to look at 1 is the largest cluster, 2 is the second
largest, 3 is the the third largest and so on. =1 The CLUSTER_PROPERTIES action with label clust1
dia: CLUSTER_DIAMETER CLUSTERScompulsory keyword 
the label of the action that does the clustering =dfs CLUSTERcompulsory keyword ( default=1 )
which cluster would you like to look at 1 is the largest cluster, 2 is the second
largest, 3 is the the third largest and so on. =1 The CLUSTER_DIAMETER action with label dia calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. =dia FILEthe name of the file on which to output these quantities =colvar The PRINT action with label

Glossary of keywords and components

Compulsory keywords

CLUSTERS	the label of the action that does the clustering
CLUSTER	( default=1 ) which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on.

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 use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation