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GMX-HYDORDER(1) GROMACS GMX-HYDORDER(1)

gmx-hydorder - Compute tetrahedrality parameters around a given atom

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>]


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 files:

Trajectory: xtc trr cpt gro g96 pdb tng
Index file
Portable xdr run input file

Options to specify output files:

X PixMap compatible matrix file
Generic output file
Generic output file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
Direction of the normal on the membrane: z, x, y
Binwidth of box mesh
tetrahedral angle parameter in Phase 1 (bulk)
tetrahedral angle parameter in Phase 2 (bulk)
Number of frames in one time-block average
Number of Height levels in 2D - XPixMaps

gmx(1)

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2019, GROMACS development team

February 15, 2019 2019.1