1GMX-ORDER(1) GROMACS GMX-ORDER(1)
2
3
4
6 gmx-order - Compute the order parameter per atom for carbon tails
7
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]unsat] [-[no]permolecule] [-[no]radial]
15 [-[no]calcdist]
16
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
27 gmx order can also give all diagonal elements of the order tensor and
28 even calculate the deuterium order parameter Scd (default). If the
29 option -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
34 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.
37
39 Options to specify input files:
40
41 -f [<.xtc/.trr/…>] (traj.xtc)
42 Trajectory: xtc trr cpt gro g96 pdb tng
43
44 -n [<.ndx>] (index.ndx)
45 Index file
46
47 -nr [<.ndx>] (index.ndx) (Optional)
48 Index file
49
50 -s [<.tpr>] (topol.tpr)
51 Portable xdr run input file
52
53 Options to specify output files:
54
55 -o [<.xvg>] (order.xvg)
56 xvgr/xmgr file
57
58 -od [<.xvg>] (deuter.xvg)
59 xvgr/xmgr file
60
61 -ob [<.pdb>] (eiwit.pdb) (Optional)
62 Protein data bank file
63
64 -os [<.xvg>] (sliced.xvg)
65 xvgr/xmgr file
66
67 -Sg [<.xvg>] (sg-ang.xvg) (Optional)
68 xvgr/xmgr file
69
70 -Sk [<.xvg>] (sk-dist.xvg) (Optional)
71 xvgr/xmgr file
72
73 -Sgsl [<.xvg>] (sg-ang-slice.xvg) (Optional)
74 xvgr/xmgr file
75
76 -Sksl [<.xvg>] (sk-dist-slice.xvg) (Optional)
77 xvgr/xmgr file
78
79 Other options:
80
81 -b <time> (0)
82 Time of first frame to read from trajectory (default unit ps)
83
84 -e <time> (0)
85 Time of last frame to read from trajectory (default unit ps)
86
87 -dt <time> (0)
88 Only use frame when t MOD dt = first time (default unit ps)
89
90 -[no]w (no)
91 View output .xvg, .xpm, .eps and .pdb files
92
93 -xvg <enum> (xmgrace)
94 xvg plot formatting: xmgrace, xmgr, none
95
96 -d <enum> (z)
97 Direction of the normal on the membrane: z, x, y
98
99 -sl <int> (1)
100 Calculate order parameter as function of box length, dividing
101 the box into this number of slices.
102
103 -[no]szonly (no)
104 Only give Sz element of order tensor. (axis can be specified
105 with -d)
106
107 -[no]unsat (no)
108 Calculate order parameters for unsaturated carbons. Note that
109 this cannot be mixed with normal order parameters.
110
111 -[no]permolecule (no)
112 Compute per-molecule Scd order parameters
113
114 -[no]radial (no)
115 Compute a radial membrane normal
116
117 -[no]calcdist (no)
118 Compute distance from a reference
119
121 gmx(1)
122
123 More information about GROMACS is available at <‐
124 http://www.gromacs.org/>.
125
127 2020, GROMACS development team
128
129
130
131
1322019.6 Feb 28, 2020 GMX-ORDER(1)