NAME

       g_dist - calculates the distances between the centers of mass of two groups

       VERSION 4.6.5

SYNOPSIS

       g_dist  -f  traj.xtc -s topol.tpr -n index.ndx -o dist.xvg -lt lifetime.xvg -[no]h -[no]version -nice int
       -b time -e time -dt time -xvg enum -[no]intra -dist real

DESCRIPTION

        g_dist can calculate the distance between the centers of mass of two groups of atoms as  a  function  of
       time. The total distance and its  x-,  y-, and  z-components are plotted.

       Or  when   -dist  is  set,  print all the atoms in group 2 that are closer than a certain distance to the
       center of mass of group 1.

       With options  -lt and  -dist the number of contacts of all atoms in  group  2  that  are  closer  than  a
       certain  distance to the center of mass of group 1 are plotted as a function of the time that the contact
       was continuously present. The  -intra switch enables calculations of  intramolecular  distances  avoiding
       distance  calculation to its periodic images. For a proper function, the molecule in the input trajectory
       should be whole (e.g. by preprocessing with  trjconv -pbc) or a matching topology should be provided. The
       -intra switch will only give meaningful results for intramolecular and not intermolecular distances.

       Other programs that calculate distances are  g_mindist and  g_bond.

FILES

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

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -n index.ndx Input, Opt.
        Index file

       -o dist.xvg Output, Opt.
        xvgr/xmgr file

       -lt lifetime.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)

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]intrano
        Calculate distances without considering periodic boundaries, e.g. intramolecular.

       -dist real 0
        Print all atoms in group 2 closer than dist to the center of mass of group 1

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                        g_dist(1)