g_dist - calculates the distances between the centers of mass of two
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg -lt
lifetime.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -dist
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
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.
-o dist.xvg Output, Opt.
-lt lifetime.xvg Output, Opt.
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)
Add specific codes (legends etc.) in the output xvg files for the
-dist real 0
Print all atoms in group 2 closer than dist to the center of mass of
More information about GROMACS is available at
Thu 16 Oct 2008 g_dist(1)