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 continously present.
Other programs that calculate distances are g_mindist and g_bond.
|-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|
|-[no]h||gmx_bool||no||Print help info and quit|
|-[no]version||gmx_bool||no||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|
|-dist||real||0||Print all atoms in group 2 closer than dist to the center of mass of group 1|