gmx sorient
Main Table of Contents VERSION 5.0.5

Synopsis

gmx sorient [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
            [-o [<.xvg>]] [-no [<.xvg>]] [-ro [<.xvg>]] [-co [<.xvg>]]
            [-rc [<.xvg>]] [-nice ] [-b

Description

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

Options

Options to specify input and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xvg>] (sori.xvg) (Output)
xvgr/xmgr file
-no [<.xvg>] (snor.xvg) (Output)
xvgr/xmgr file
-ro [<.xvg>] (sord.xvg) (Output)
xvgr/xmgr file
-co [<.xvg>] (scum.xvg) (Output)
xvgr/xmgr file
-rc [<.xvg>] (scount.xvg) (Output)
xvgr/xmgr file
Other options:

-nice <int> (19)
Set the nicelevel
-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 postion
-[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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