xenial (1) gmx-h2order.1.gz

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