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)