table of contents
g_h2order(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_h2order(1) |
NAME¶
g_h2order - computes the orientation of water moleculesSYNOPSIS¶
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 intDESCRIPTION¶
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 InputTrajectory: xtc trr trj gro g96 pdb cpt
Index file
Index file
Run input file: tpr tpb tpa
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Take the normal on the membrane in direction X, Y or Z.
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)Mon 4 Apr 2011 |