Compute tetrahedrality parameters around a given atom
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>]
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 to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input)
Index file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-o [<.xpm> [...]] (intf.xpm) (Output)
X PixMap compatible matrix file
-or [<.out> [...]] (raw.out) (Output, Optional)
Generic output file
-Spect [<.out> [...]] (intfspect.out) (Output, Optional)
Generic output file
Other options:
-nice <int> (19)
Set the nicelevel
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (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
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