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       g_mindist - calculates the minimum distance between two groups

       VERSION 4.0.1


       g_mindist  -f  traj.xtc  -s  topol.tpr -n index.ndx -od mindist.xvg -on
       numcont.xvg -o atm-pair.out -ox mindist.xtc -or  mindistres.xvg  -[no]h
       -nice  int  -b  time  -e  time  -dt  time  -tu  enum  -[no]w  -[no]xvgr
       -[no]matrix -[no]max -d real -[no]pi -[no]split -ng int -[no]pbc


       g_mindist computes the distance between one group and a number of other
       groups.  Both  the minimum distance (between any pair of atoms from the
       respective groups) and the number of contacts within a  given  distance
       are written to two separate output files.  With  -or, minimum distances
       to each residue in the first group are  determined  and  plotted  as  a
       function of reisdue number.

       With  option  -pi the minimum distance of a group to its periodic image
       is plotted. This is useful for checking  if  a  protein  has  seen  its
       periodic image during a simulation. Only one shift in each direction is
       considered, giving a total of 26 shifts.  It  also  plots  the  maximum
       distance within the group and the lengths of the three box vectors.

       Other programs that calculate distances are  g_dist and  g_bond.


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

       -s topol.tpr Input, Opt.
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -od mindist.xvg Output
        xvgr/xmgr file

       -on numcont.xvg Output, Opt.
        xvgr/xmgr file

       -o atm-pair.out Output, Opt.
        Generic output file

       -ox mindist.xtc Output, Opt.
        Trajectory: xtc trr trj gro g96 pdb

       -or mindistres.xvg Output, Opt.
        xvgr/xmgr 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

        Calculate half a matrix of group-group distances

        Calculate *maximum* distance instead of minimum

       -d real 0.6
        Distance for contacts

        Calculate minimum distance with periodic images

        Split graph where time is zero

       -ng int 1
        Number of secondary groups to compute distance to a central group

        Take periodic boundary conditions into account



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                   g_mindist(1)