gmx hydorder

	gmx hydorder
	Main Table of Contents	VERSION 5.0.6

Synopsis

gmx hydorder [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr/.tpb/...>]]
             [-o [<.xpm> [...]]] [-or [<.out> [...]]] [-Spect [<.out> [...]]]
             [-nice ] [-b ] [-e ] [-dt ] [-[no]w]
             [-d ] [-bw ] [-sgang1 ] [-sgang2 ]
             [-tblock ] [-nlevel ]

Description

gmx hydorder computes the tetrahedrality order parameters around a given atom. Both angle an distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details.

gmx hydorder calculates the order parameter in a 3d-mesh in the box, and with 2 phases in the box gives the user the option to define a 2D interface in time separating the faces by specifying parameters -sgang1 and -sgang2 (it is important to select these judiciously).

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
-s [<.tpr/.tpb/...>] (topol.tpr) (Input): Run input file: tpr tpb tpa
-o [<.xpm> [...]] (intf.xpm) (Output): X PixMap compatible matrix file
-or [<.out> [...]] (raw.out) (Output, Optional): Generic output file
-Spect [<.out> [...]] (intfspect.out) (Output, Optional): Generic output 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
-d <enum> (z): Direction of the normal on the membrane: z, x, y
-bw <real> (1): Binwidth of box mesh
-sgang1 <real> (1): tetrahedral angle parameter in Phase 1 (bulk)
-sgang2 <real> (1): tetrahedral angle parameter in Phase 2 (bulk)
-tblock <int> (1): Number of frames in one time-block average
-nlevel <int> (100): Number of Height levels in 2D - XPixMaps

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