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gmx-hydorder(1)			GROMACS Manual		       gmx-hydorder(1)

NAME
       gmx-hydorder - Compute tetrahedrality parameters around a given atom

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

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

SEE ALSO
       gromacs(7)

       More   information  about  GROMACS  is  available  at  <http://www.gro‐
       macs.org/>.

VERSION 5.0.6						       gmx-hydorder(1)

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