NAME

       gmx-h2order - Compute the orientation of water molecules

SYNOPSIS

          gmx h2order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nm [<.ndx>]]
                      [-s [<.tpr>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
                      [-dt <time>] [-[no]w] [-xvg <enum>] [-d <string>]
                      [-sl <int>]

DESCRIPTION

       gmx  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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -n [<.ndx>] (index.ndx)
              Index file

       -nm [<.ndx>] (index.ndx) (Optional)
              Index file

       -s [<.tpr>] (topol.tpr)
              Portable xdr run input file

       Options to specify output files:

       -o [<.xvg>] (order.xvg)
              xvgr/xmgr file

       Other options:

       -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]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum>
              xvg plot formatting: xmgrace, xmgr, 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 ISSUES

       • 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

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team