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: 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)
Time of first frame to read from trajectory (default unit ps)
- -e <time> (0)
Time of last frame to read from trajectory (default unit ps)
- -dt <time> (0)
Only use frame when t MOD dt = first time (default unit 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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