1g_order(1) GROMACS suite, VERSION 4.5 g_order(1)
2
6 g_order - computes the order parameter per atom for carbon tails
7 VERSION 4.5
9
11 g_order -f traj.xtc -n index.ndx -nr index.ndx -s topol.tpr -o
12 order.xvg -od deuter.xvg -ob eiwit.pdb -os sliced.xvg -Sg sg-ang.xvg
13 -Sk sk-dist.xvg -Sgsl sg-ang-slice.xvg -Sksl sk-dist-slice.xvg -[no]h
14 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d
15 enum -sl int -[no]szonly -[no]unsat -[no]permolecule -[no]radial
16 -[no]calcdist
17
19 Compute the order parameter per atom for carbon tails. For atom i the
20 vector i-1, i+1 is used together with an axis. The index file should
21 contain only the groups to be used for calculations, with each group of
22 equivalent carbons along the relevant acyl chain in its own group.
23 There should not be any generic groups (like System, Protein) in the
24 index file to avoid confusing the program (this is not relevant to
25 tetrahedral order parameters however, which only work for water any‐
26 way).
27 The program can also give all diagonal elements of the order tensor and
30 even calculate the deuterium order parameter Scd (default). If the
31 option -szonly is given, only one order tensor component (specified by
32 the -d option) is given and the order parameter per slice is calculated
33 as well. If -szonly is not selected, all diagonal elements and the deu‐
34 terium order parameter is given.
35 The tetrahedrality order parameters can be determined around an atom.
37 Both angle an distance order parameters are calculated. See P.-L. Chau
38 and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details.
39
43 -f traj.xtc Input
44 Trajectory: xtc trr trj gro g96 pdb cpt
45 -n index.ndx Input
47 Index file
48 -nr index.ndx Input
50 Index file
51 -s topol.tpr Input
53 Run input file: tpr tpb tpa
54 -o order.xvg Output
56 xvgr/xmgr file
57 -od deuter.xvg Output
59 xvgr/xmgr file
60 -ob eiwit.pdb Output
62 Protein data bank file
63 -os sliced.xvg Output
65 xvgr/xmgr file
66 -Sg sg-ang.xvg Output, Opt.
68 xvgr/xmgr file
69 -Sk sk-dist.xvg Output, Opt.
71 xvgr/xmgr file
72 -Sgsl sg-ang-slice.xvg Output, Opt.
74 xvgr/xmgr file
75 -Sksl sk-dist-slice.xvg Output, Opt.
77 xvgr/xmgr file
78
81 -[no]hno
82 Print help info and quit
83 -[no]versionno
85 Print version info and quit
86 -nice int 19
88 Set the nicelevel
89 -b time 0
91 First frame (ps) to read from trajectory
92 -e time 0
94 Last frame (ps) to read from trajectory
95 -dt time 0
97 Only use frame when t MOD dt = first time (ps)
98 -[no]wno
100 View output xvg, xpm, eps and pdb files
101 -xvg enum xmgrace
103 xvg plot formatting: xmgrace, xmgr or none
104 -d enum z
106 Direction of the normal on the membrane: z, x or y
107 -sl int 1
109 Calculate order parameter as function of boxlength, dividing the box
110 in nr slices.
111 -[no]szonlyno
113 Only give Sz element of order tensor. (axis can be specified with -d)
114 -[no]unsatno
116 Calculate order parameters for unsaturated carbons. Note that this
117 cannot be mixed with normal order parameters.
118 -[no]permoleculeno
120 Compute per-molecule Scd order parameters
121 -[no]radialno
123 Compute a radial membrane normal
124 -[no]calcdistno
126 Compute distance from a reference (currently defined only for radial
127 and permolecule)
128
131 gromacs(7)
132 More information about GROMACS is available at <http://www.gro‐
134 macs.org/>.
135 Thu 26 Aug 2010 g_order(1)