# g_cluster(1) [debian man page]

g_cluster(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_cluster(1)NAME

g_cluster - clusters structures VERSION 4.5.4-dev-20110404-bc5695cSYNOPSIS

g_clustertraj.xtc-ftopol.tpr-sindex.ndx-nrmsd.xpm-dmrmsd-clust.xpm-ocluster.log-grmsd-dist.xvg-distrmsd-eig.xvg-evclust-size.xvg-szclust-trans.xpm-trclust-trans.xvg-ntrclust-id.xvg-clidclusters.pdb -[no]h -[no]version-clint-nicetime-btime-etime-dtenum -[no]w-tuenum -[no]dista-xvgint-nlevelsreal -[no]fit-cutoffreal-maxint -[no]av-skipint-wclint-nstreal-rmsminenum-methodint -[no]binary-minstructint-Mint-Pint-seedint-niterreal -[no]pbc-kTDESCRIPTION

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 theoption. 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 clus- ter 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:-dmwrites the RMSD values in the upper left half of the matrix and a graphical depiction of the clusters in the lower right half When-o= 1 the graphical depiction is black when two structures are in the same cluster. When-minstruct1 different colors will be used for each cluster.-minstructwrites 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:-gwrites the RMSD distribution.-distwrites the eigenvectors of the RMSD matrix diagonalization.-evwrites the cluster sizes.-szwrites a matrix of the number transitions between cluster pairs.-trwrites the total number of transitions to or from each cluster.-ntrwrites the cluster number as a function of time.-clidwrites 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-cl, depends on-wcland -rmsmin).-nstFILES

traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt-ftopol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb-sindex.ndx Input, Opt. Index file-nrmsd.xpm Input, Opt. X PixMap compatible matrix file-dmrmsd-clust.xpm Output X PixMap compatible matrix file-ocluster.log Output Log file-grmsd-dist.xvg Output, Opt. xvgr/xmgr file-distrmsd-eig.xvg Output, Opt. xvgr/xmgr file-evclust-size.xvg Output, Opt. xvgr/xmgr file-szclust-trans.xpm Output, Opt. X PixMap compatible matrix file-trclust-trans.xvg Output, Opt. xvgr/xmgr file-ntrclust-id.xvg Output, Opt. xvgr/xmgr file-clidclusters.pdb Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt-clOTHER OPTIONS

-[no]hno Print help info and quit -[no]versionno Print version info and quitint 19 Set the nicelevel-nicetime 0 First frame (ps) to read from trajectory-btime 0 Last frame (ps) to read from trajectory-etime 0 Only use frame when t MOD dt = first time (ps)-dtenum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files-tuenum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]distano Use RMSD of distances instead of RMS deviation-xvgint 40 Discretize RMSD matrix in levels-nlevelsreal 0.1 RMSD cut-off (nm) for two structures to be neighbor -[no]fityes Use least squares fitting before RMSD calculation-cutoffreal-maxMaximum level in RMSD matrix-1int 1 Only analyze every nr-th frame -[no]avno Write average iso middle structure for each cluster-skipint 0 Write all structures for first clusters to numbered files-wclint 1 Only write all structures if more than per cluster-nstreal 0 minimum rms difference with rest of cluster for writing structures-rmsminenum linkage Method for cluster determination: linkage, jarvis-patrick, monte-carlo, diagonalization or gromos-methodint 1 Minimum number of structures in cluster for coloring in the .xpm file -[no]binaryno Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by-minstruct-cutoffint 10 Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff-Mint 3 Number of identical nearest neighbors required to form a cluster-Pint 1993 Random number seed for Monte Carlo clustering algorithm-seedint 10000 Number of iterations for MC-niterreal 0.001 Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) -[no]pbcyes PBC check-kTSEE ALSO

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_cluster(1)