.. _gmx hydorder: gmx hydorder ============ Synopsis -------- .. parsed-literal:: gmx hydorder [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-o` :emphasis:`[<.xpm> [...]]`] [:strong:`-or` :emphasis:`[<.out> [...]]`] [:strong:`-Spect` :emphasis:`[<.out> [...]]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-d` :emphasis:`<enum>`] [:strong:`-bw` :emphasis:`<real>`] [:strong:`-sgang1` :emphasis:`<real>`] [:strong:`-sgang2` :emphasis:`<real>`] [:strong:`-tblock` :emphasis:`<int>`] [:strong:`-nlevel` :emphasis:`<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: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`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 :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <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 .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at <http://www.gromacs.org/>.