1GMX-HYDORDER(1) GROMACS GMX-HYDORDER(1)
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6 gmx-hydorder - Compute tetrahedrality parameters around a given atom
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9 gmx hydorder [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
10 [-o [<.xpm> [...]]] [-or [<.out> [...]]]
11 [-Spect [<.out> [...]]] [-b <time>] [-e <time>]
12 [-dt <time>] [-[no]w] [-d <enum>] [-bw <real>]
13 [-sgang1 <real>] [-sgang2 <real>] [-tblock <int>]
14 [-nlevel <int>]
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17 gmx hydorder computes the tetrahedrality order parameters around a
18 given atom. Both angle an distance order parameters are calculated. See
19 P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for
20 more details.
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22 gmx hydorder calculates the order parameter in a 3d-mesh in the box,
23 and with 2 phases in the box gives the user the option to define a 2D
24 interface in time separating the faces by specifying parameters -sgang1
25 and -sgang2 (it is important to select these judiciously).
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28 Options to specify input files:
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30 -f [<.xtc/.trr/...>] (traj.xtc)
31 Trajectory: xtc trr cpt gro g96 pdb tng
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33 -n [<.ndx>] (index.ndx)
34 Index file
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36 -s [<.tpr>] (topol.tpr)
37 Portable xdr run input file
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39 Options to specify output files:
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41 -o [<.xpm> [...]] (intf.xpm)
42 X PixMap compatible matrix file
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44 -or [<.out> [...]] (raw.out) (Optional)
45 Generic output file
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47 -Spect [<.out> [...]] (intfspect.out) (Optional)
48 Generic output file
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50 Other options:
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52 -b <time> (0)
53 Time of first frame to read from trajectory (default unit ps)
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55 -e <time> (0)
56 Time of last frame to read from trajectory (default unit ps)
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58 -dt <time> (0)
59 Only use frame when t MOD dt = first time (default unit ps)
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61 -[no]w (no)
62 View output .xvg, .xpm, .eps and .pdb files
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64 -d <enum> (z)
65 Direction of the normal on the membrane: z, x, y
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67 -bw <real> (1)
68 Binwidth of box mesh
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70 -sgang1 <real> (1)
71 tetrahedral angle parameter in Phase 1 (bulk)
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73 -sgang2 <real> (1)
74 tetrahedral angle parameter in Phase 2 (bulk)
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76 -tblock <int> (1)
77 Number of frames in one time-block average
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79 -nlevel <int> (100)
80 Number of Height levels in 2D - XPixMaps
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83 gmx(1)
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85 More information about GROMACS is available at <‐
86 http://www.gromacs.org/>.
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89 2022, GROMACS development team
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942022.3 Sep 02, 2022 GMX-HYDORDER(1)