.TH gmx-sorient 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-sorient \- Analyze solvent orientation around solutes

.SH SYNOPSIS
gmx sorient [\-f [<.xtc/.trr/...>]] [\-s [<.tpr/.tpb/...>]]
            [\-n [<.ndx>]] [\-o [<.xvg>]] [\-no [<.xvg>]] [\-ro [<.xvg>]]
            [\-co [<.xvg>]] [\-rc [<.xvg>]] [\-nice <int>] [\-b <time>]
            [\-e <time>] [\-dt <time>] [\-[no]w] [\-xvg <enum>]
            [\-[no]com] [\-[no]v23] [\-rmin <real>] [\-rmax <real>]
            [\-cbin <real>] [\-rbin <real>] [\-[no]pbc]

.SH DESCRIPTION
\fBgmx sorient\fR 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 \fB\-v23\fR 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 \fB\-rmin\fR and \fB\-rmax\fR are considered for \fB\-o\fR and \fB\-no\fR each frame.

\fB\-o\fR: distribtion of cos(theta_1) for rmin=r=rmax.

\fB\-no\fR: distribution of cos(theta_2) for rmin=r=rmax.

\fB\-ro\fR: cos(theta_1) and 3cos(2theta_2)\-1 as a function of the distance.

\fB\-co\fR: the sum over all solvent molecules within distance r of cos(theta_1) and 3cos(2(theta_2)\-1) as a function of r.

\fB\-rc\fR: the distribution of the solvent molecules as a function of r

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-o" " [<.xvg>] (sori.xvg) (Output)"
    xvgr/xmgr file

.BI "\-no" " [<.xvg>] (snor.xvg) (Output)"
    xvgr/xmgr file

.BI "\-ro" " [<.xvg>] (sord.xvg) (Output)"
    xvgr/xmgr file

.BI "\-co" " [<.xvg>] (scum.xvg) (Output)"
    xvgr/xmgr file

.BI "\-rc" " [<.xvg>] (scount.xvg) (Output)"
    xvgr/xmgr file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-[no]com" "  (no)"
    Use the center of mass as the reference postion

.BI "\-[no]v23" "  (no)"
    Use the vector between atoms 2 and 3

.BI "\-rmin" " <real> (0)"
    Minimum distance (nm)

.BI "\-rmax" " <real> (0.5)"
    Maximum distance (nm)

.BI "\-cbin" " <real> (0.02)"
    Binwidth for the cosine

.BI "\-rbin" " <real> (0.02)"
    Binwidth for r (nm)

.BI "\-[no]pbc" "  (no)"
    Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.


.SH SEE ALSO
.BR gromacs(7)

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