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       g_h2order - computes the orientation of water molecules

       VERSION 4.0.1


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


       Compute  the  orientation of water molecules with respect to the normal
       of the box. The program determines the  average  cosine  of  the  angle
       between  de  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.


       -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


        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)

        View output xvg, xpm, eps and pdb files

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -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 nr slices.


       - The program assigns whole water molecules to a slice,  based  on  the
       firstatom  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.



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                   g_h2order(1)