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NAME

       g_sorient - analyzes solvent orientation around solutes

       VERSION 4.0.1

SYNOPSIS

       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 -nice  int  -b
       time  -e  time  -dt  time -[no]w -[no]xvgr -[no]com -[no]v23 -rmin real
       -rmax real -cbin real -rbin real -[no]pbc

DESCRIPTION

       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 molecule: theta1:  the  angle  with  the
       vector  from  the  first  atom  of the solvent molecule to the midpoint
       between atoms 2 and 3.

       theta2: 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(theta1) for rmin=r=rmax.

        -no: distribution of cos(theta2) for rmin=r=rmax.

        -ro: cos(theta1) and 3cos2(theta2)-1 as a function of the distance.

         -co:  the  sum  over  all  solvent  molecules  within  distance  r of
       cos(theta1) and 3cos2(theta2)-1 as a function of r.

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

FILES

       -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

OTHER OPTIONS

       -[no]hno
        Print help 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)

       -[no]wno
        View output xvg, xpm, eps and pdb files

       -[no]xvgryes
        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -[no]comno
        Use the center of mass as the reference postion

       -[no]v23no
        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]pbcno
        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/>.

                                Thu 16 Oct 2008                   g_sorient(1)