gmx h2order

	gmx h2order
	Main Table of Contents	VERSION 5.0.7

Synopsis

gmx h2order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nm [<.ndx>]]
            [-s [<.tpr/.tpb/...>]] [-o [<.xvg>]] [-nice ] [-b ]
            [-e ] [-dt ] [-[no]w] [-xvg ] [-d ]
            [-sl ]

Description

gmx 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.

Options

Options to specify input and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input): Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input): Index file
-nm [<.ndx>] (index.ndx) (Input, Optional): Index file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input): Run input file: tpr tpb tpa
-o [<.xvg>] (order.xvg) (Output): xvgr/xmgr file

Other options:

-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]w (no): View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace): xvg plot formatting: xmgrace, xmgr, none
-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 this number of slices.

Known Issues

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.

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