gmx-sorient man page
gmx-sorient — Analyze solvent orientation around solutes
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 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)
Options to specify output files:
- -o [<.xvg>] (sori.xvg)
- -no [<.xvg>] (snor.xvg)
- -ro [<.xvg>] (sord.xvg)
- -co [<.xvg>] (scum.xvg)
- -rc [<.xvg>] (scount.xvg)
- -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 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.
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2017, GROMACS development team