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 -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.

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

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