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
-v23is 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
-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
-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:
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
Use the center of mass as the reference position
Use the vector between atoms 2 and 3
Minimum distance (nm)
Maximum distance (nm)
Binwidth for the cosine
Binwidth for r (nm)
Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.