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GMX-HYDORDER(1)			    GROMACS		       GMX-HYDORDER(1)

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

SYNOPSIS
	  gmx hydorder [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s	[<.tpr>]]
		       [-o [<.xpm> [...]]] [-or	[<.out>	[...]]]
		       [-Spect [<.out> [...]]] [-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	files:

       -f [<.xtc/.trr/...>] (traj.xtc)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -n [<.ndx>] (index.ndx)
	      Index file

       -s [<.tpr>] (topol.tpr)
	      Portable xdr run input file

       Options to specify output files:

       -o [<.xpm> [...]] (intf.xpm)
	      X	PixMap compatible matrix file

       -or [<.out> [...]] (raw.out) (Optional)
	      Generic output file

       -Spect [<.out> [...]] (intfspect.out) (Optional)
	      Generic output file

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit 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
       gmx(1)

       More	information    about	GROMACS	   is	 available    at    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2025, GROMACS development team

2025.0				 Feb 10, 2025		       GMX-HYDORDER(1)

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