.TH gmx-hydorder 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom

.SH 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>]

.SH DESCRIPTION
\fBgmx hydorder\fR 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.

\fBgmx hydorder\fR 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 \fB\-sgang1\fR and \fB\-sgang2\fR (it is important to select these judiciously).

.SH OPTIONS
Options to specify input and output files:

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

.BI "\-n" " [<.ndx>] (index.ndx) (Input)"
    Index file

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Run input file: tpr tpb tpa

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

.BI "\-or" " [<.out> [...]] (raw.out) (Output, Optional)"
    Generic output file

.BI "\-Spect" " [<.out> [...]] (intfspect.out) (Output, Optional)"
    Generic output file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-d" " <enum> (z)"
    Direction of the normal on the membrane: z, x, y

.BI "\-bw" " <real> (1)"
    Binwidth of box mesh

.BI "\-sgang1" " <real> (1)"
    tetrahedral angle parameter in Phase 1 (bulk)

.BI "\-sgang2" " <real> (1)"
    tetrahedral angle parameter in Phase 2 (bulk)

.BI "\-tblock" " <int> (1)"
    Number of frames in one time\-block average

.BI "\-nlevel" " <int> (100)"
    Number of Height levels in 2D \- XPixMaps


.SH SEE ALSO
.BR gromacs(7)

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