g_mindist

| ## g_mindist Main Table of Contents | VERSION 4.5 Thu 26 Aug 2010

### Description

g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With the `-group` option a contact of an atom an other group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. With `-or`, minimum distances to each residue in the first group are determined and plotted as a function of residue number.

With option `-pi` the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors.

Other programs that calculate distances are `g_dist` and `g_bond`.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.xtc` | Input | Trajectory: xtc trr trj gro g96 pdb cpt
`-s` | `topol.tpr` | Input, Opt. | Structure+mass(db): tpr tpb tpa gro g96 pdb
`-n` | `index.ndx` | Input, Opt. | Index file
`-od` | `mindist.xvg` | Output | xvgr/xmgr file
`-on` | `numcont.xvg` | Output, Opt. | xvgr/xmgr file
`-o` | `atm-pair.out` | Output, Opt. | Generic output file
`-ox` | `mindist.xtc` | Output, Opt. | Trajectory: xtc trr trj gro g96 pdb
`-or` | `mindistres.xvg` | Output, Opt. | xvgr/xmgr file

### Other options

option | type | default | description
--- | --- | --- | ---
`-[no]h` | gmx_bool | `no` | Print help info and quit
`-[no]version` | gmx_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)
`-tu` | enum | `ps` | Time unit: `fs`, `ps`, `ns`, `us`, `ms` or `s`
`-[no]w` | gmx_bool | `no` | View output xvg, xpm, eps and pdb files
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-[no]matrix` | gmx_bool | `no` | Calculate half a matrix of group-group distances
`-[no]max` | gmx_bool | `no` | Calculate *maximum* distance instead of minimum
`-d` | real | `0.6` | Distance for contacts
`-[no]group` | gmx_bool | `no` | Count contacts with multiple atoms in the first group as one
`-[no]pi` | gmx_bool | `no` | Calculate minimum distance with periodic images
`-[no]split` | gmx_bool | `no` | Split graph where time is zero
`-ng` | int | `1` | Number of secondary groups to compute distance to a central group
`-[no]pbc` | gmx_bool | `yes` | Take periodic boundary conditions into account
`-[no]respertime` | gmx_bool | `no` | When writing per-residue distances, write distance for each time point
`-[no]printresname` | gmx_bool | `no` | Write residue names

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