trjorder

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

### Description

trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option `-z`). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number `-da` in the molecule and all the atoms in the reference group. The center of mass of the molecules can be used instead of a reference atom by setting `-da` to 0. All atoms in the trajectory are written to the output trajectory.

trjorder can be useful for e.g. analyzing the n waters closest to a protein. In that case the reference group would be the protein and the group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can be used with any Gromacs program to analyze the n closest waters.

If the output file is a pdb file, the distance to the reference target will be stored in the B-factor field in order to color with e.g. rasmol.

With option `-nshell` the number of molecules within a shell of radius `-r` around the reference group are printed.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.xtc` | Input | Trajectory: xtc trr trj gro g96 pdb cpt
`-s` | `topol.tpr` | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb
`-n` | `index.ndx` | Input, Opt. | Index file
`-o` | `ordered.xtc` | Output, Opt. | Trajectory: xtc trr trj gro g96 pdb
`-nshell` | `nshell.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)
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-na` | int | `3` | Number of atoms in a molecule
`-da` | int | `1` | Atom used for the distance calculation, 0 is COM
`-[no]com` | gmx_bool | `no` | Use the distance to the center of mass of the reference group
`-r` | real | `0` | Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
`-[no]z` | gmx_bool | `no` | Order molecules on z-coordinate

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