| VERSION 3.1 |
g_cluster can cluster structures with several different methods. Distances between structures can be determined from a trajectory or read from an XPM matrix file with the -dm option. RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures.
full linkage: add a structure to a cluster when its distance to any element of the cluster is less than cutoff.
Jarvis Patrick: add a structure to a cluster when this structure and a structure in the cluster have each other as neighbors and they have a least P neighbors in common. The neighbors of a structure are the M closest structures or all structures within cutoff.
Monte Carlo: reorder the RMSD matrix using Monte Carlo.
diagonalization: diagonalize the RMSD matrix.
gromos: use algorithm as described in Daura
When the clustering algorithm assigns each structure to exactly one cluster (full linkage, Jarvis Patrick and gromos) and a trajectory file is supplied, the structure with the smallest average distance to the others or the average structure or all structures for each cluster will be written to a trajectory file. When writing all structures, separate numbered files are made for each cluster.
Two output files are always written:
-o writes the RMSD values in the upper left half of the matrix
and a graphical depiction of the clusters in the lower right half
(depends on -max and -keepfree).
-g writes information on the options used and a detailed list
of all clusters and their members.
Additionally, a number of optional output files can be written:
-dist writes the RMSD distribution.
-ev writes the eigenvectors of the RMSD matrix
diagonalization.
-sz writes the cluster sizes.
-tr writes a matrix of the number transitions between
cluster pairs.
-ntr writes the total number of transitions to or from
each cluster.
-clid writes the cluster number as a function of time.
-cl writes average (with option -av) or central
structure of each cluster or writes numbered files with cluster members
for a selected set of clusters (with option -wcl, depends on
-nst and -rmsmin).
option | filename | type | description |
---|---|---|---|
-f | traj.xtc | Input, Opt. | Generic trajectory: xtc trr trj gro g96 pdb |