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]
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 to specify input files:
Options to specify output files:
Other options: