g_h2order - computes the orientation of water molecules
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
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.
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input
-nm index.ndx Input, Opt.
-s topol.tpr Input
Run input file: tpr tpb tpa
-o order.xvg Output
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)
View output xvg, xpm, eps and pdb files
Add specific codes (legends etc.) in the output xvg files for the
-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.
- 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.
More information about GROMACS is available at
Thu 16 Oct 2008 g_h2order(1)