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:
Options to specify output files:
Other options: