NAME
g_h2order - computes the orientation of water molecules
VERSION 4.0.1
SYNOPSIS
g_h2order -f traj.xtc -n index.ndx -nm index.ndx -s topol.tpr -o
order.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d
string -sl int
DESCRIPTION
Compute the orientation of water molecules with respect to the normal
of the box. The program determines the average cosine of the angle
between de 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
-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
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-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
firstatom 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/>.
Thu 16 Oct 2008 g_h2order(1)