| 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¶
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT¶
2023, GROMACS development team
| February 3, 2023 | 2022.5 |