NAME

       g_clustsize - calculate size distributions of atomic clusters

       VERSION 4.6.5

SYNOPSIS

       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  -[no]version
       -nice  int  -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

       This program computes the size distributions of molecular/atomic clusters 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 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.

FILES

       -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

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version 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:  fs,  ps,  ns,  us,  ms or  s

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

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

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

       -[no]pbcyes
        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

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                   g_clustsize(1)