Provided by: gromacs-data_4.6.5-1build1_all bug


       g_sorient - analyzes solvent orientation around solutes

       VERSION 4.6.5


       g_sorient  -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co
       scum.xvg -rc scount.xvg -[no]h -[no]version -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


         g_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

       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


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -o sori.xvg Output
        xvgr/xmgr file

       -no snor.xvg Output
        xvgr/xmgr file

       -ro sord.xvg Output
        xvgr/xmgr file

       -co scum.xvg Output
        xvgr/xmgr file

       -rc scount.xvg Output
        xvgr/xmgr file


        Print help info and quit

        Print version info and quit

       -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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

        Use the center of mass as the reference postion

        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)

        Check PBC for the center of mass calculation. Only necessary when  your  reference  group
       consists of several molecules.



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                             g_sorient(1)