g_dist

Main Table of Contents

VERSION 4.6.3
Fri 5 Jul 2013


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. 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.

Files

optionfilenametypedescription
-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

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no 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]intra bool no 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


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