---
name: "gmx-hydorder"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-hydorder"
---

# gmx-hydorder(1)

Compute tetrahedrality parameters around a given atom

## NAME

gmx-hydorder - Compute tetrahedrality parameters around a given atom

## SYNOPSIS

```
gmx hydorder [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
             [-o [<.xpm> [...]]] [-or [<.out> [...]]]
             [-Spect [<.out> [...]]] [-b <time>] [-e <time>]
             [-dt <time>] [-[no]w] [-d <enum>] [-bw <real>]
             [-sgang1 <real>] [-sgang2 <real>] [-tblock <int>]
             [-nlevel <int>]
```

## DESCRIPTION

**gmx hydorder** computes the tetrahedrality order parameters around a given 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.

**gmx hydorder** calculates the order parameter in a 3d-mesh in the box, and with 2 phases in the box gives the user the option to define a 2D interface in time separating the faces by specifying parameters **-sgang1** and **-sgang2** (it is important to select these judiciously).

## OPTIONS

Options to specify input files:

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc)**

  Trajectory: *xtc* *trr* *cpt* *gro* *g96* *pdb* *tng*

- **-n \[\<.ndx\>\] (index.ndx)**

  Index file

- **-s \[\<.tpr\>\] (topol.tpr)**

  Portable xdr run input file

Options to specify output files:

- **-o \[\<.xpm\> \[...\]\] (intf.xpm)**

  X PixMap compatible matrix file

- **-or \[\<.out\> \[...\]\] (raw.out) (Optional)**

  Generic output file

- **-Spect \[\<.out\> \[...\]\] (intfspect.out) (Optional)**

  Generic output file

Other options:

- **-b \<time\> (0)**

  Time of first frame to read from trajectory (default unit ps)

- **-e \<time\> (0)**

  Time of last frame to read from trajectory (default unit ps)

- **-dt \<time\> (0)**

  Only use frame when t MOD dt = first time (default unit ps)

- **-\[no\]w (no)**

  View output *.xvg*, *.xpm*, *.eps* and *.pdb* files

- **-d \<enum\> (z)**

  Direction of the normal on the membrane: z, x, y

- **-bw \<real\> (1)**

  Binwidth of box mesh

- **-sgang1 \<real\> (1)**

  tetrahedral angle parameter in Phase 1 (bulk)

- **-sgang2 \<real\> (1)**

  tetrahedral angle parameter in Phase 2 (bulk)

- **-tblock \<int\> (1)**

  Number of frames in one time-block average

- **-nlevel \<int\> (100)**

  Number of Height levels in 2D - XPixMaps

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team