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g_spatial - calculates the spatial distribution function (more control than g_sdf)VERSION4.0.1

g_spatial-ftraj.xtc-stopol.tpr-nindex.ndx-dmrmsd.xpm-ormsd-clust.xpm-gcluster.log-distrmsd-dist.xvg-evrmsd-eig.xvg-szclust-size.xvg-trclust-trans.xpm-ntrclust-trans.xvg-clidclust-id.xvg-clclusters.pdb-[no]h-niceint-btime-etime-dttime-tuenum-[no]w-[no]xvgr-[no]dista-nlevelsint-cutoffreal-[no]fit-maxreal-skipint-[no]av-wclint-nstint-rmsminreal-methodenum-minstructint-[no]binary-Mint-Pint-seedint-niterint-kTreal

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-dmoption. 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 thancutoff. 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 leastPneighbors in common. The neighbors of a structure are the M closest structures or all structures withincutoff. Monte Carlo: reorder the RMSD matrix using Monte Carlo. diagonalization: diagonalize the RMSD matrix. gromos: use algorithm as described in Dauraetal.(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 eleminate 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:-owrites 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-minstruct1 different colors will be used for each cluster.-gwrites 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:-distwrites the RMSD distribution.-evwrites the eigenvectors of the RMSD matrix diagonalization.-szwrites the cluster sizes.-trwrites a matrix of the number transitions between cluster pairs.-ntrwrites the total number of transitions to or from each cluster.-clidwrites the cluster number as a function of time.-clwrites 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-nstand-rmsmin).

-ftraj.xtcInput,Opt.Trajectory: xtc trr trj gro g96 pdb cpt-stopol.tprInput,Opt.Structure+mass(db): tpr tpb tpa gro g96 pdb-nindex.ndxInput,Opt.Index file-dmrmsd.xpmInput,Opt.X PixMap compatible matrix file-ormsd-clust.xpmOutputX PixMap compatible matrix file-gcluster.logOutputLog file-distrmsd-dist.xvgOutput,Opt.xvgr/xmgr file-evrmsd-eig.xvgOutput,Opt.xvgr/xmgr file-szclust-size.xvgOutput,Opt.xvgr/xmgr file-trclust-trans.xpmOutput,Opt.X PixMap compatible matrix file-ntrclust-trans.xvgOutput,Opt.xvgr/xmgr file-clidclust-id.xvgOutput,Opt.xvgr/xmgr file-clclusters.pdbOutput,Opt.Trajectory: xtc trr trj gro g96 pdb cpt

-[no]hnoPrint help info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-tuenumpsTime unit:ps,fs,ns,us,msors-[no]wnoView output xvg, xpm, eps and pdb files-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-[no]distanoUse RMSD of distances instead of RMS deviation-nlevelsint40Discretize RMSD matrix in levels-cutoffreal0.1RMSD cut-off (nm) for two structures to be neighbor-[no]fityesUse least squares fitting before RMSD calculation-maxreal-1Maximum level in RMSD matrix-skipint1Only analyze every nr-th frame-[no]avnoWrite average iso middle structure for each cluster-wclint0Write all structures for first clusters to numbered files-nstint1Only write all structures if more than per cluster-rmsminreal0minimum rms difference with rest of cluster for writing structures-methodenumlinkageMethod for cluster determination:linkage,jarvis-patrick,monte-carlo,diagonalizationorgromos-minstructint1Minimum number of structures in cluster for coloring in the xpm file-[no]binarynoTreat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff-Mint10Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff-Pint3Number of identical nearest neighbors required to form a cluster-seedint1993Random number seed for Monte Carlo clustering algorithm-niterint10000Number of iterations for MC-kTreal0.001Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps)

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_spatial(1)