NAME

       g_mindist - calculates the minimum distance between two groups

       VERSION 4.6.5

SYNOPSIS

       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 -[no]version -nice int -b time -e time -dt  time  -tu  enum  -[no]w
       -xvg  enum  -[no]matrix  -[no]max  -d real -[no]group -[no]pi -[no]split -ng int -[no]pbc -[no]respertime
       -[no]printresname

DESCRIPTION

        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 the  -group option a contact of an atom in
       another group with multiple atoms in the first group is counted as one contact  instead  of  as  multiple
       contacts.   With  -or, minimum distances to each residue in the first group are determined and plotted as
       a function of residue 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.

FILES

       -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

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

       -[no]matrixno
        Calculate half a matrix of group-group distances

       -[no]maxno
        Calculate *maximum* distance instead of minimum

       -d real 0.6
        Distance for contacts

       -[no]groupno
        Count contacts with multiple atoms in the first group as one

       -[no]pino
        Calculate minimum distance with periodic images

       -[no]splitno
        Split graph where time is zero

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

       -[no]pbcyes
        Take periodic boundary conditions into account

       -[no]respertimeno
        When writing per-residue distances, write distance for each time point

       -[no]printresnameno
        Write residue names

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                     g_mindist(1)