1GMX-ORDER(1) GROMACS GMX-ORDER(1)
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6 gmx-order - Compute the order parameter per atom for carbon tails
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9 gmx order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nr [<.ndx>]]
10 [-s [<.tpr>]] [-o [<.xvg>]] [-od [<.xvg>]] [-ob [<.pdb>]]
11 [-os [<.xvg>]] [-Sg [<.xvg>]] [-Sk [<.xvg>]]
12 [-Sgsl [<.xvg>]] [-Sksl [<.xvg>]] [-b <time>] [-e <time>]
13 [-dt <time>] [-[no]w] [-xvg <enum>] [-d <enum>] [-sl <int>]
14 [-[no]szonly] [-[no]permolecule] [-[no]radial]
15 [-[no]calcdist]
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18 gmx order computes the order parameter per atom for carbon tails. For
19 atom i the vector i-1, i+1 is used together with an axis. The index
20 file should contain only the groups to be used for calculations, with
21 each group of equivalent carbons along the relevant acyl chain in its
22 own group. There should not be any generic groups (like System, Pro‐
23 tein) in the index file to avoid confusing the program (this is not
24 relevant to tetrahedral order parameters however, which only work for
25 water anyway).
26 gmx order can also give all diagonal elements of the order tensor and
28 even calculate the deuterium order parameter Scd (default). If the op‐
29 tion -szonly is given, only one order tensor component (specified by
30 the -d option) is given and the order parameter per slice is calculated
31 as well. If -szonly is not selected, all diagonal elements and the deu‐
32 terium order parameter is given.
33 The tetrahedrality order parameters can be determined around an atom.
35 Both angle an distance order parameters are calculated. See P.-L. Chau
36 and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details.
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39 Options to specify input files:
40 -f [<.xtc/.trr/...>] (traj.xtc)
42 Trajectory: xtc trr cpt gro g96 pdb tng
43 -n [<.ndx>] (index.ndx)
45 Index file
46 -nr [<.ndx>] (index.ndx) (Optional)
48 Index file
49 -s [<.tpr>] (topol.tpr)
51 Portable xdr run input file
52 Options to specify output files:
54 -o [<.xvg>] (order.xvg)
56 xvgr/xmgr file
57 -od [<.xvg>] (deuter.xvg)
59 xvgr/xmgr file
60 -ob [<.pdb>] (eiwit.pdb) (Optional)
62 Protein data bank file
63 -os [<.xvg>] (sliced.xvg)
65 xvgr/xmgr file
66 -Sg [<.xvg>] (sg-ang.xvg) (Optional)
68 xvgr/xmgr file
69 -Sk [<.xvg>] (sk-dist.xvg) (Optional)
71 xvgr/xmgr file
72 -Sgsl [<.xvg>] (sg-ang-slice.xvg) (Optional)
74 xvgr/xmgr file
75 -Sksl [<.xvg>] (sk-dist-slice.xvg) (Optional)
77 xvgr/xmgr file
78 Other options:
80 -b <time> (0)
82 Time of first frame to read from trajectory (default unit ps)
83 -e <time> (0)
85 Time of last frame to read from trajectory (default unit ps)
86 -dt <time> (0)
88 Only use frame when t MOD dt = first time (default unit ps)
89 -[no]w (no)
91 View output .xvg, .xpm, .eps and .pdb files
92 -xvg <enum> (xmgrace)
94 xvg plot formatting: xmgrace, xmgr, none
95 -d <enum> (z)
97 Direction of the normal on the membrane: z, x, y
98 -sl <int> (1)
100 Calculate order parameter as function of box length, dividing
101 the box into this number of slices.
102 -[no]szonly (no)
104 Only give Sz element of order tensor. (axis can be specified
105 with -d)
106 -[no]permolecule (no)
108 Compute per-molecule Scd order parameters
109 -[no]radial (no)
111 Compute a radial membrane normal
112 -[no]calcdist (no)
114 Compute distance from a reference
115
117 • This tool only works for saturated carbons and united atom force
118 fields.
119 • For anything else, it is highly recommended to use a different analy‐
121 sis method!
122 • The option -unsat claimed to do analysis for unsaturated carbons
124 • this but hasn't worked ever since it was added and has thus been re‐
126 moved.
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129 gmx(1)
130 More information about GROMACS is available at <‐
132 http://www.gromacs.org/>.
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135 2022, GROMACS development team
1362022.2 Jun 16, 2022 GMX-ORDER(1)