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 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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (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 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

       gmx(1)

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

COPYRIGHT

       2024, GROMACS development team