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:
θ_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. θ_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(θ_1) for rmin<=r<=rmax.
-no: distribution of cos(θ_2) for rmin<=r<=rmax.
-ro: <cos(θ_1)> and <3cos(^2θ_2)-1> as a function of the distance.
-co: the sum over all solvent molecules within distance r of cos(θ_1) and 3cos(^2(θ_2)-1) as a function of r.
-rc: the distribution of the solvent molecules as a function of r