Main Table of Contents

Wed 13 Nov 2013


g_cluster can cluster structures using 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.

single 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 et al. (Angew. Chem. Int. Ed. 1999, 38, pp 236-240). Count number of neighbors using cut-off, take structure with largest number of neighbors with all its neighbors as cluster and eliminate it from the pool of clusters. Repeat for remaining structures in pool.

When the clustering algorithm assigns each structure to exactly one cluster (single 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 When -minstruct = 1 the graphical depiction is black when two structures are in the same cluster. When -minstruct > 1 different colors will be used for each cluster.
-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). The center of a cluster is the structure with the smallest average RMSD from all other structures of the cluster.


-f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-dm rmsd.xpm Input, Opt. X PixMap compatible matrix file
-o rmsd-clust.xpm Output X PixMap compatible matrix file
-g cluster.log Output Log file
-dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file
-ev rmsd-eig.xvg Output, Opt. xvgr/xmgr file
-sz clust-size.xvg Output, Opt. xvgr/xmgr file
-tr clust-trans.xpm Output, Opt. X PixMap compatible matrix file
-ntr clust-trans.xvg Output, Opt. xvgr/xmgr file
-clid clust-id.xvg Output, Opt. xvgr/xmgr file
-cl clusters.pdb Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]dista bool no Use RMSD of distances instead of RMS deviation
-nlevels int 40 Discretize RMSD matrix in this number of levels
-cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor
-[no]fit bool yes Use least squares fitting before RMSD calculation
-max real -1 Maximum level in RMSD matrix
-skip int 1 Only analyze every nr-th frame
-[no]av bool no Write average iso middle structure for each cluster
-wcl int 0 Write the structures for this number of clusters to numbered files
-nst int 1 Only write all structures if more than this number of structures per cluster
-rmsmin real 0 minimum rms difference with rest of cluster for writing structures
-method enum linkage Method for cluster determination: linkage, jarvis-patrick, monte-carlo, diagonalization or gromos
-minstruct int 1 Minimum number of structures in cluster for coloring in the .xpm file
-[no]binary bool no Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff
-M int 10 Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff
-P int 3 Number of identical nearest neighbors required to form a cluster
-seed int 1993 Random number seed for Monte Carlo clustering algorithm
-niter int 10000 Number of iterations for MC
-kT real 0.001 Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps)
-[no]pbc bool yes PBC check