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gmx-sorient(1)                  GROMACS Manual                  gmx-sorient(1)

NAME
       gmx-sorient - Analyze solvent orientation around solutes

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]

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:

       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: distribtion 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
       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.

SEE ALSO
       gromacs(7)

       More information about GROMACS is available at
       <http://www.gromacs.org/>.

VERSION 5.0.6                                                   gmx-sorient(1)