g_h2order_d (1) - Linux Manuals
g_h2order_d: computes the orientation of water molecules
NAMEg_h2order - computes the orientation of water molecules
SYNOPSISg_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
DESCRIPTIONCompute 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
-nice int 19
-b time 0
-e time 0
-dt time 0
-d string Z
-sl int 0
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.
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