GMX-HYDORDER(1) GROMACS GMX-HYDORDER(1) 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 h5md -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/>. COPYRIGHT 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-HYDORDER(1)
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