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)