g_dist

NAME

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

SYNOPSIS

g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -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.

Other programs that calculate distances are g_mindist

and g_bond

FILES

-f traj.xtc Input
Generic trajectory: xtc trr trj gro g96 pdb

-s topol.tpr Input
Generic run input: tpr tpb tpa xml

-n index.ndx Input, Opt.
Index file

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

OTHER OPTIONS

-[no]h no
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)

-[no]xvgr yes
Add specific codes (legends etc.) in the output xvg files for the xmgrace program

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