g_dist_d (1) Linux Manual Page

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

VERSION 4.0.1

Synopsis

g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg -lt lifetime.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.

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

-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]xvgryes
 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

See Also

gromacs(7)

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