---
name: "g_sorient_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-sorient"
---

# g\_sorient\_d(1)

Analyze solvent orientation around solutes

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

## NAME

gmx-sorient - Analyze solvent orientation around solutes

## SYNOPSIS

gmx sorient \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
             \[-n \[\<.ndx\>\]\] \[-o \[\<.xvg\>\]\] \[-no \[\<.xvg\>\]\] \[-ro \[\<.xvg\>\]\]\
             \[-co \[\<.xvg\>\]\] \[-rc \[\<.xvg\>\]\] \[-nice \<int\>\] \[-b \<time\>\]\
             \[-e \<time\>\] \[-dt \<time\>\] \[-\[no\]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**: distribtion 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 and output files:

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

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

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

**-o** *\[\<.xvg\>\] (sori.xvg) (Output)*\
     xvgr/xmgr file

**-no** *\[\<.xvg\>\] (snor.xvg) (Output)*\
     xvgr/xmgr file

**-ro** *\[\<.xvg\>\] (sord.xvg) (Output)*\
     xvgr/xmgr file

**-co** *\[\<.xvg\>\] (scum.xvg) (Output)*\
     xvgr/xmgr file

**-rc** *\[\<.xvg\>\] (scount.xvg) (Output)*\
     xvgr/xmgr 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

**-xvg** *\<enum\> (xmgrace)*\
     xvg plot formatting: xmgrace, xmgr, none

**-\[no\]com**  *(no)*\
     Use the center of mass as the reference postion

**-\[no\]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

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

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