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GMX-CLUSTER(1)			    GROMACS			GMX-CLUSTER(1)

NAME
       gmx-cluster - Cluster structures

SYNOPSIS
	  gmx cluster [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n	[<.ndx>]]
		      [-dm [<.xpm>]] [-om [<.xpm>]] [-o	[<.xpm>]] [-g [<.log>]]
		      [-dist [<.xvg>]] [-ev [<.xvg>]] [-conv [<.xvg>]]
		      [-sz [<.xvg>]] [-tr [<.xpm>]] [-ntr [<.xvg>]]
		      [-clid [<.xvg>]] [-cl [<.xtc/.trr/...>]]
		      [-clndx [<.ndx>]]	[-b <time>] [-e	<time>]	[-dt <time>]
		      [-tu <enum>] [-[no]w] [-xvg <enum>] [-[no]dista]
		      [-nlevels	<int>] [-cutoff	<real>]	[-[no]fit]
		      [-max <real>] [-skip <int>] [-[no]av] [-wcl <int>]
		      [-nst <int>] [-rmsmin <real>] [-method <enum>]
		      [-minstruct <int>] [-[no]binary] [-M <int>] [-P <int>]
		      [-seed <int>] [-niter <int>] [-nrandom <int>]
		      [-kT <real>] [-[no]pbc]

DESCRIPTION
       gmx  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  such  that  the
       order  of  the  frames is using the smallest possible increments.  With
       this it is possible to make a smooth animation going from one structure
       to another with the largest possible (e.g.) RMSD	between	them,  however
       the  intermediate  steps	 should	be as small as possible.  Applications
       could be	to visualize a potential of mean force ensemble	of simulations
       or a pulling simulation.	Obviously the user has to prepare the  trajec-
       tory  well (e.g.	by not superimposing frames).  The final result	can be
       inspect visually	by looking at the matrix .xpm file, which should  vary
       smoothly	from bottom to top.

       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  re-
       maining 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, sep-
       arate 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	struc-
	    tures are in the same cluster.  When -minstruct > 1	different col-
	    ors	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	 clus-
	    ter.

	   -clid writes the cluster number as a function of time.

	   -clndx  writes  the	frame numbers corresponding to the clusters to
	    the	specified index	file to	be read	into trjconv.

	   -cl	writes average (with option -av) or central structure of  each
	    cluster  or	 writes	 numbered files	with cluster members for a se-
	    lected set of clusters (with option	 -wcl,	depends	 on  -nst  and
	    -rmsmin). The center of a cluster is the structure with the	small-
	    est	average	RMSD from all other structures of the cluster.

OPTIONS
       Options to specify input	files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr)
	      Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
	      Index file

       -dm [<.xpm>] (rmsd.xpm) (Optional)
	      X	PixMap compatible matrix file

       Options to specify output files:

       -om [<.xpm>] (rmsd-raw.xpm)
	      X	PixMap compatible matrix file

       -o [<.xpm>] (rmsd-clust.xpm)
	      X	PixMap compatible matrix file

       -g [<.log>] (cluster.log)
	      Log file

       -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
	      xvgr/xmgr	file

       -ev [<.xvg>] (rmsd-eig.xvg) (Optional)
	      xvgr/xmgr	file

       -conv [<.xvg>] (mc-conv.xvg) (Optional)
	      xvgr/xmgr	file

       -sz [<.xvg>] (clust-size.xvg) (Optional)
	      xvgr/xmgr	file

       -tr [<.xpm>] (clust-trans.xpm) (Optional)
	      X	PixMap compatible matrix file

       -ntr [<.xvg>] (clust-trans.xvg) (Optional)
	      xvgr/xmgr	file

       -clid [<.xvg>] (clust-id.xvg) (Optional)
	      xvgr/xmgr	file

       -cl [<.xtc/.trr/...>] (clusters.pdb) (Optional)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -clndx [<.ndx>] (clusters.ndx) (Optional)
	      Index file

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit ps)

       -tu <enum> (ps)
	      Unit for time values: fs,	ps, ns,	us, ms,	s

       -[no]w (no)
	      View output .xvg,	.xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
	      xvg plot formatting: xmgrace, xmgr, none

       -[no]dista (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	(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 (no)
	      Write average instead of 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	struc-
	      tures

       -method <enum> (linkage)
	      Method   for  cluster  determination:  linkage,  jarvis-patrick,
	      monte-carlo, diagonalization, gromos

       -minstruct <int>	(1)
	      Minimum number of	structures in cluster for coloring in the .xpm
	      file

       -[no]binary (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 algo-
	      rithm, 0 is use cutoff

       -P <int>	(3)
	      Number of	identical nearest neighbors required to	form a cluster

       -seed <int> (0)
	      Random number seed for Monte Carlo clustering algorithm (0 means
	      generate)

       -niter <int> (10000)
	      Number of	iterations for MC

       -nrandom	<int> (0)
	      The first	iterations for MC may  be  done	 complete  random,  to
	      shuffle the frames

       -kT <real> (0.001)
	      Boltzmann	 weighting  factor  for	Monte Carlo optimization (zero
	      turns off	uphill steps)

       -[no]pbc	(yes)
	      PBC check

SEE ALSO
       gmx(1)

       More    information    about    GROMACS	  is	available    at	    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2025, GROMACS development team

2025.0				 Feb 10, 2025			GMX-CLUSTER(1)

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