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 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

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.