debian man page for g_h2order

g_h2order(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_h2order(1)

NAME
       g_h2order - computes the orientation of water molecules

       VERSION 4.5.4-dev-20110404-bc5695c

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 nr 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 4 Apr 2011						      g_h2order(1)