NAME

       g_h2order - computes the orientation of water molecules

       VERSION 4.6.5

SYNOPSIS

       g_h2order  -f traj.xtc -n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -[no]version -nice int
       -b time -e time -dt time -[no]w -xvg enum -d string -sl int

DESCRIPTION

        g_h2order computes the orientation of water molecules with respect to the normal of the box. The program
       determines the average cosine of the angle between the dipole moment of water and an axis of the box. The
       box is divided in slices and the average orientation per  slice  is  printed.   Each  water  molecule  is
       assigned  to  a  slice, per time frame, based on the position of the oxygen. When  -nm is used, the angle
       between the water dipole and the axis from the center of mass to the oxygen is calculated instead of  the
       angle between the dipole and a box axis.

FILES

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

       -n index.ndx Input
        Index file

       -nm index.ndx Input, Opt.
        Index file

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -o order.xvg Output
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        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)

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

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

       -d string Z
        Take the normal on the membrane in direction X, Y or Z.

       -sl int 0
        Calculate order parameter as function of boxlength, dividing the box in this number of slices.

KNOWN PROBLEMS

       -  The  program  assigns  whole water molecules to a slice, based on the first atom of three in the index
       file group. It assumes an order O,H,H. Name is not important, but the order is. If  this  demand  is  not
       met, assigning molecules to slices is different.

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                     g_h2order(1)