## g_dist

Main Table of Contents

VERSION 4.6
Sat 19 Jan 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 <it>x</it>-, <it>y</it>-, and <it>z</it>-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

option | filename | type | description
--- | --- | --- | ---
`-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

option | type | default | description
--- | --- | --- | ---
`-[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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