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

### Description

Compute the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. The index file should contain only the groups to be used for calculations, with each group of equivalent carbons along the relevant acyl chain in its own group. There should not be any generic groups (like System, Protein) in the index file to avoid confusing the program (this is not relevant to tetrahedral order parameters however, which only work for water anyway).

The program can also give all diagonal elements of the order tensor and even calculate the deuterium order parameter Scd (default). If the option -szonly is given, only one order tensor component (specified by the -d option) is given and the order parameter per slice is calculated as well. If -szonly is not selected, all diagonal elements and the deuterium order parameter is given.

The tetrahedrality order parameters can be determined around an atom. Both angle an distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.xtc` | Input | Trajectory: xtc trr trj gro g96 pdb cpt
`-n` | `index.ndx` | Input | Index file
`-nr` | `index.ndx` | Input | Index file
`-s` | `topol.tpr` | Input | Run input file: tpr tpb tpa
`-o` | `order.xvg` | Output | xvgr/xmgr file
`-od` | `deuter.xvg` | Output | xvgr/xmgr file
`-ob` | `eiwit.pdb` | Output | Protein data bank file
`-os` | `sliced.xvg` | Output | xvgr/xmgr file
`-Sg` | `sg-ang.xvg` | Output, Opt. | xvgr/xmgr file
`-Sk` | `sk-dist.xvg` | Output, Opt. | xvgr/xmgr file
`-Sgsl` | `sg-ang-slice.xvg` | Output, Opt. | xvgr/xmgr file
`-Sksl` | `sk-dist-slice.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`
`-d` | enum | `z` | Direction of the normal on the membrane: `z`, `x` or `y`
`-sl` | int | `1` | Calculate order parameter as function of boxlength, dividing the box in #nr slices.
`-[no]szonly` | gmx_bool | `no` | Only give Sz element of order tensor. (axis can be specified with -d)
`-[no]unsat` | gmx_bool | `no` | Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.
`-[no]permolecule` | gmx_bool | `no` | Compute per-molecule Scd order parameters
`-[no]radial` | gmx_bool | `no` | Compute a radial membrane normal
`-[no]calcdist` | gmx_bool | `no` | Compute distance from a reference (currently defined only for radial and permolecule)

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