Exploiting contact matrices

A contact 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. There are various ways of defining whether a pair of atoms/molecules are adjacent or not. For example we can say two atoms are adjacent if the distance between them is less than some cutoff. Alternatively, if we have a have a pair of molecules, we might state they are adjacent if their centers of mass are within a certain cutoff and if the two molecules have the same orientation. Two electronegative atoms might be said to be adjacent if there is a hydrogen bond between them. For these reasons then PLUMED contains all of the following methods for calculating an adjacency matrix

ALIGNED_MATRIX | Adjacency matrix in which two molecule are adjacent if they are within a certain cutoff and if they have the same orientation. |

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

HBOND_MATRIX | Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them. |

HBPAMM_MATRIX | Adjacency matrix in which two electronegative atoms are adjacent if they are hydrogen bonded |

SMAC_MATRIX | Adjacency matrix in which two molecules are adjacent if they are within a certain cutoff and if the angle between them is within certain ranges. |

TOPOLOGY_MATRIX | Adjacency matrix in which two atoms are adjacent if they are connected topologically |

Once you have calculated an adjacency matrix you can then perform any one of the following operations on this object in order to reduce it to a scalar number or a set of connected components.

CLUSTER_WITHSURFACE | Take a connected component that was found using a clustering algorithm and create a new cluster that contains those atoms that are in the cluster together with those atoms that are within a certain cutoff of the cluster. |

COLUMNSUMS | Sum the columns of a contact matrix |

DFSCLUSTERING | Find the connected components of the matrix using the depth first search clustering algorithm. |

ROWSUMS | Sum the rows of a adjacency matrix. |

SPRINT | Calculate SPRINT topological variables from an adjacency matrix. |

If the function you have chosen reduces your contact matrix to a set of connected components you then need a method to convert these connected components into a scalar number or to output this information to a file. The various things that you can do with a set of connected components are listed below:

CLUSTER_DIAMETER | Print out the diameter of one of the connected components |

CLUSTER_DISTRIBUTION | Calculate functions of the distribution of properties in your connected components. |

CLUSTER_NATOMS | Gives the number of atoms in the connected component |

CLUSTER_PROPERTIES | Calculate properties of the distribution of some quantities that are part of a connected component |

DUMPGRAPH | Write out the connectivity of the nodes in the graph in dot format. |

OUTPUT_CLUSTER | Output the indices of the atoms in one of the clusters identified by a clustering object |