Man page - gmx-hydorder(1)
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apt-get install gromacs-data
Manual
GMX-HYDORDER
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
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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