SYNOPSISg_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 -dist real
DESCRIPTIONg_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.
Other programs that calculate distances are g_mindist and g_bond.
FILES-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
Run input file: tpr tpb tpa
Print help info and quit
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