---
name: "g_hydorder_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-hydorder"
---

# g\_hydorder\_d(1)

Compute tetrahedrality parameters around a given atom

Part of [gmx-hydorder(1)](/gmx-hydorder/1.md).

## NAME

gmx-hydorder - Compute tetrahedrality parameters around a given atom

## SYNOPSIS

gmx hydorder \[-f \[\<.xtc/.trr/...\>\]\] \[-n \[\<.ndx\>\]\]\
              \[-s \[\<.tpr/.tpb/...\>\]\] \[-o \[\<.xpm\> \[...\]\]\]\
              \[-or \[\<.out\> \[...\]\]\] \[-Spect \[\<.out\> \[...\]\]\]\
              \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\]\
              \[-\[no\]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 and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

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

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Run input file: tpr tpb tpa

**-o** *\[\<.xpm\> \[...\]\] (intf.xpm) (Output)*\
     X PixMap compatible matrix file

**-or** *\[\<.out\> \[...\]\] (raw.out) (Output, Optional)*\
     Generic output file

**-Spect** *\[\<.out\> \[...\]\] (intfspect.out) (Output, Optional)*\
     Generic output file

Other options:

**-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**  *(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

**[gromacs(7)](/gromacs/7.md)**

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