# gmx sorient#

## 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.