CLUSTER_NATOMS

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. |

Gives the number of atoms in the connected component

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 analysing 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 number 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 is not differentiable. As such it cannot be used as a collective variable in a biased simulation.

- 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 parallelize |

LOWMEM | ( default=off ) lower the memory requirements |

TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |

- 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 and then the number of atoms in the largest cluster is found. This quantity is then output to a file called colvar

# Calculate coordination numbers c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} # Select coordination numbers that are more than 2.0 cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM # Build a contact matrix mat: CONTACT_MATRIX ATOMS=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} # Find largest cluster dfs: DFSCLUSTERING MATRIX=mat clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 nat: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1 PRINT ARG=nat FILE=COLVAR