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GMX-H2ORDER(1)			     GROMACS			  GMX-H2ORDER(1)

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 <enum>]
		    [-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  di-
     vided in slices and the average orientation per slice is printed.	Each wa-
     ter  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 an-
     gle 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 h5md

     -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)
	    Time of first frame to read from trajectory (default unit ps)

     -e <time> (0)
	    Time of last frame to read from trajectory (default unit ps)

     -dt <time> (0)
	    Only use frame when t MOD dt = first time (default unit ps)

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

     -xvg <enum> (xmgrace)
	    xvg plot formatting: xmgrace, xmgr, none

     -d <enum> (Z)
	    Take the normal on the membrane in direction X, Y or Z.: Z, Y, X

     -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
     2026, GROMACS development team

2026.3				  Jun 25, 2026			  GMX-H2ORDER(1)
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