Provided by: gromacs-data_4.6.5-1build1_all bug


       g_clustsize - calculate size distributions of atomic clusters

       VERSION 4.6.5


       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


       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


       -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

        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

        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

        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 <>.

                                          Mon 2 Dec 2013                           g_clustsize(1)