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

# gmx-sorient(1)

Analyze solvent orientation around solutes

## NAME

gmx-sorient - Analyze solvent orientation around solutes

## SYNOPSIS

```
gmx sorient [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
            [-o [<.xvg>]] [-no [<.xvg>]] [-ro [<.xvg>]]
            [-co [<.xvg>]] [-rc [<.xvg>]] [-b <time>] [-e <time>]
            [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]com] [-[no]v23]
            [-rmin <real>] [-rmax <real>] [-cbin <real>]
            [-rbin <real>] [-[no]pbc]
```

## DESCRIPTION

**gmx sorient** analyzes solvent orientation around solutes. It calculates two angles between the vector from one or more reference positions to the first atom of each solvent molecule:

- •

  theta\_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3.

- •

  theta\_2: the angle with the normal of the solvent plane, defined by the same three atoms, or, when the option **-v23** is set, the angle with the vector between atoms 2 and 3.

The reference can be a set of atoms or the center of mass of a set of atoms. The group of solvent atoms should consist of 3 atoms per solvent molecule. Only solvent molecules between **-rmin** and **-rmax** are considered for **-o** and **-no** each frame.

**-o**: distribution of cos(theta\_1) for rmin\<=r\<=rmax.

**-no**: distribution of cos(theta\_2) for rmin\<=r\<=rmax.

**-ro**: \<cos(theta\_1)\> and \<3cos(^2theta\_2)-1\> as a function of the distance.

**-co**: the sum over all solvent molecules within distance r of cos(theta\_1) and 3cos(^2(theta\_2)-1) as a function of r.

**-rc**: the distribution of the solvent molecules as a function of r

## OPTIONS

Options to specify input files:

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

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

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

  Structure+mass(db): *tpr* *gro* *g96* *pdb* brk ent

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

  Index file

Options to specify output files:

- **-o \[\<.xvg\>\] (sori.xvg)**

  xvgr/xmgr file

- **-no \[\<.xvg\>\] (snor.xvg)**

  xvgr/xmgr file

- **-ro \[\<.xvg\>\] (sord.xvg)**

  xvgr/xmgr file

- **-co \[\<.xvg\>\] (scum.xvg)**

  xvgr/xmgr file

- **-rc \[\<.xvg\>\] (scount.xvg)**

  xvgr/xmgr 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

- **-xvg \<enum\> (xmgrace)**

  xvg plot formatting: xmgrace, xmgr, none

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

  Use the center of mass as the reference position

- **-\[no\]v23 (no)**

  Use the vector between atoms 2 and 3

- **-rmin \<real\> (0)**

  Minimum distance (nm)

- **-rmax \<real\> (0.5)**

  Maximum distance (nm)

- **-cbin \<real\> (0.02)**

  Binwidth for the cosine

- **-rbin \<real\> (0.02)**

  Binwidth for r (nm)

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

  Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team