gmx-hydorder - Compute tetrahedrality parameters around a given atom

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-HYDORDER(1)

gmxhydorder  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.

       gmxhydorder  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).

       gmx-hydorder - Compute tetrahedrality parameters around a given atom

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-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

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

          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>]