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GMX-CLUSTSIZE(1)		    GROMACS		      GMX-CLUSTSIZE(1)

NAME
       gmx-clustsize - Calculate size distributions of atomic clusters

SYNOPSIS
	  gmx clustsize	[-f [_.xtc/.trr/..._]] [-s [_.tpr_]] [-n [_.ndx_]]
		       [-o [_.xpm_]] [-ow [_.xpm_]] [-nc [_.xvg_]]
		       [-mc [_.xvg_]] [-ac [_.xvg_]] [-hc [_.xvg_]]
		       [-temp [_.xvg_]]	[-mcn [_.ndx_]]	[-b _time_] [-e	_time_]
		       [-dt _time_] [-tu _enum_] [-[no]w] [-xvg	_enum_]
		       [-cut _real_] [-[no]mol]	[-[no]pbc] [-nskip _int_]
		       [-nlevels _int_]	[-ndf _int_] [-rgblo _vector_]
		       [-rgbhi _vector_]

DESCRIPTION
       gmx clustsize computes the size distributions of	molecular/atomic clus-
       ters in the gas phase. The output is given in the form of an .xpm file.
       The total number	of clusters is written to an .xvg file.

       When  the  -mol	option is given	clusters will be made out of molecules
       rather than atoms, which	allows clustering of large molecules.  In this
       case an index file would	still contain atom numbers or your calculation
       will die	with a SEGV.

       When velocities are present in your trajectory, the temperature of  the
       largest	cluster	 will be printed in a separate .xvg file assuming that
       the particles are free to move. If you are  using  constraints,	please
       correct	the  temperature.  For	instance water simulated with SHAKE or
       SETTLE will yield a temperature that is 1.5 times too low. You can com-
       pensate	for this with the -ndf option. Remember	to take	the removal of
       center of mass motion into account.

       The -mc option will produce an index file containing the	 atom  numbers
       of the largest cluster.

OPTIONS
       Options to specify input	files:

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

       -s [<.tpr>] (topol.tpr) (Optional)
	      Portable xdr run input file

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

       Options to specify output files:

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

       -ow [<.xpm>] (csizew.xpm)
	      X	PixMap compatible matrix file

       -nc [<.xvg>] (nclust.xvg)
	      xvgr/xmgr	file

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

       -ac [<.xvg>] (avclust.xvg)
	      xvgr/xmgr	file

       -hc [<.xvg>] (histo-clust.xvg)
	      xvgr/xmgr	file

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

       -mcn [<.ndx>] (maxclust.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

       -cut <real> (0.35)
	      Largest distance (nm) to be considered in	a cluster

       -[no]mol	(no)
	      Cluster molecules	rather than atoms (needs .tpr file)

       -[no]pbc	(yes)
	      Use periodic boundary conditions

       -nskip <int> (0)
	      Number of	frames to skip between writing

       -nlevels	<int> (20)
	      Number of	levels of grey in .xpm output

       -ndf <int> (-1)
	      Number  of  degrees of freedom of	the entire system for tempera-
	      ture calculation.	If not set, the	number of atoms	times three is
	      used.

       -rgblo <vector> (1 1 0)
	      RGB values for the color of the lowest occupied cluster size

       -rgbhi <vector> (0 0 1)
	      RGB values for the color of the highest occupied cluster size

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020		      GMX-CLUSTSIZE(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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