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/>.

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