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       g_clustsize - calculate size distributions of atomic clusters

       VERSION 4.0.1


       g_clustsize  -f  traj.xtc  -s  topol.tpr  -n index.ndx -o csize.xpm -ow
       csizew.xpm  -nc  nclust.xvg  -mc  maxclust.xvg  -ac   avclust.xvg   -hc
       histo-clust.xvg  -temp  temp.xvg  -mcn maxclust.ndx -[no]h -nice int -b
       time -e time -dt time -tu enum  -[no]w  -[no]xvgr  -cut  real  -[no]mol
       -[no]pbc -nskip int -nlevels int -ndf int -rgblo vector -rgbhi vector


       This  program  computes  the  size  distributions  of  molecular/atomic
       clusters in the gas phase. The output is given in the  form  of  a  XPM
       file.  The total number of clusters is written to a 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
       calculcation 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
       compensate  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.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input, Opt.
        Portable xdr run input file

       -n index.ndx Input, Opt.
        Index file

       -o csize.xpm Output
        X PixMap compatible matrix file

       -ow csizew.xpm Output
        X PixMap compatible matrix file

       -nc nclust.xvg Output
        xvgr/xmgr file

       -mc maxclust.xvg Output
        xvgr/xmgr file

       -ac avclust.xvg Output
        xvgr/xmgr file

       -hc histo-clust.xvg Output
        xvgr/xmgr file

       -temp temp.xvg Output, Opt.
        xvgr/xmgr file

       -mcn maxclust.ndx Output, Opt.
        Index file


        Print help 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:  ps,  fs,  ns,  us,  ms or  s

        View output xvg, xpm, eps and pdb files

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

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

        Cluster molecules rather than atoms (needs tpr file)

        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  temperature
       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



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                 g_clustsize(1)