1GMX-HYDORDER(1)                     GROMACS                    GMX-HYDORDER(1)
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NAME

6       gmx-hydorder - Compute tetrahedrality parameters around a given atom
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SYNOPSIS

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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DESCRIPTION

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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OPTIONS

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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SEE ALSO

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       2019, GROMACS development team
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942019.2                           Apr 16, 2019                  GMX-HYDORDER(1)
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