gmx hydorder#

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