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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
-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)
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COPYRIGHT

2018, GROMACS development team
June 14, 2018 2018.2