g_dist(1) - Linux man page

Name

g_dist - calculates the distances between the centers of mass of two

groups

VERSION 4.5.4-dev-20110404-bc5695c

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 continously 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