.TH g_h2order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_h2order - computes the orientation of water molecules

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_h2order\fP
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-nm" " index.ndx "
.BI "\-s" " topol.tpr "
.BI "\-o" " order.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-d" " string "
.BI "\-sl" " int "
.SH DESCRIPTION
\&\fB g_h2order\fR 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 \fB \-nm\fR 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.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-nm" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-o" " order.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-d"  " string" " Z" 
 Take the normal on the membrane in direction X, Y or Z.

.BI "\-sl"  " int" " 0" 
 Calculate order parameter as function of boxlength, dividing the box in nr slices.

.SH 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.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.