g_bond

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

### Description

g_bond makes a distribution of bond lengths. If all is well a gaussian distribution should be made when using a harmonic potential. Bonds are read from a single group in the index file in order i1-j1 i2-j2 through in-jn.

`-tol` gives the half-width of the distribution as a fraction of the bondlength (`-blen`). That means, for a bond of 0.2 a tol of 0.1 gives a distribution from 0.18 to 0.22.

Option `-d` plots all the distances as a function of time. This requires a structure file for the atom and residue names in the output. If however the option `-averdist` is given (as well or separately) the average bond length is plotted instead.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.xtc` | Input | Trajectory: xtc trr trj gro g96 pdb cpt
`-n` | `index.ndx` | Input | Index file
`-s` | `topol.tpr` | Input, Opt. | Structure+mass(db): tpr tpb tpa gro g96 pdb
`-o` | `bonds.xvg` | Output | xvgr/xmgr file
`-l` | `bonds.log` | Output, Opt. | Log file
`-d` | `distance.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)
`-[no]w` | gmx_bool | `no` | View output xvg, xpm, eps and pdb files
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-blen` | real | `-1` | Bond length. By default length of first bond
`-tol` | real | `0.1` | Half width of distribution as fraction of blen
`-[no]aver` | gmx_bool | `yes` | Average bond length distributions
`-[no]averdist` | gmx_bool | `yes` | Average distances (turns on -d)

### Known problems

- It should be possible to get bond information from the topology.

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