Provided by: gromacs-data_4.6.5-1build1_all
g_dist - calculates the distances between the centers of mass of two groups VERSION 4.6.5
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 -[no]intra -dist real
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. The -intra switch enables calculations of intramolecular distances avoiding distance calculation to its periodic images. For a proper function, the molecule in the input trajectory should be whole (e.g. by preprocessing with trjconv -pbc) or a matching topology should be provided. The -intra switch will only give meaningful results for intramolecular and not intermolecular distances. Other programs that calculate distances are g_mindist and g_bond.
-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
-[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 -[no]intrano Calculate distances without considering periodic boundaries, e.g. intramolecular. -dist real 0 Print all atoms in group 2 closer than dist to the center of mass of group 1
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_dist(1)