1GMX-ORDER(1)                        GROMACS                       GMX-ORDER(1)
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NAME

6       gmx-order - Compute the order parameter per atom for carbon tails
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SYNOPSIS

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]
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DESCRIPTION

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).
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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.
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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.
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OPTIONS

39       Options to specify input files:
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41       -f [<.xtc/.trr/…>] (traj.xtc)
42              Trajectory: xtc trr cpt gro g96 pdb tng
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44       -n [<.ndx>] (index.ndx)
45              Index file
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47       -nr [<.ndx>] (index.ndx) (Optional)
48              Index file
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50       -s [<.tpr>] (topol.tpr)
51              Portable xdr run input file
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53       Options to specify output files:
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55       -o [<.xvg>] (order.xvg)
56              xvgr/xmgr file
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58       -od [<.xvg>] (deuter.xvg)
59              xvgr/xmgr file
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61       -ob [<.pdb>] (eiwit.pdb) (Optional)
62              Protein data bank file
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64       -os [<.xvg>] (sliced.xvg)
65              xvgr/xmgr file
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67       -Sg [<.xvg>] (sg-ang.xvg) (Optional)
68              xvgr/xmgr file
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70       -Sk [<.xvg>] (sk-dist.xvg) (Optional)
71              xvgr/xmgr file
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73       -Sgsl [<.xvg>] (sg-ang-slice.xvg) (Optional)
74              xvgr/xmgr file
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76       -Sksl [<.xvg>] (sk-dist-slice.xvg) (Optional)
77              xvgr/xmgr file
78
79       Other options:
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81       -b <time> (0)
82              Time of first frame to read from trajectory (default unit ps)
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84       -e <time> (0)
85              Time of last frame to read from trajectory (default unit ps)
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87       -dt <time> (0)
88              Only use frame when t MOD dt = first time (default unit ps)
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90       -[no]w (no)
91              View output .xvg, .xpm, .eps and .pdb files
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93       -xvg <enum> (xmgrace)
94              xvg plot formatting: xmgrace, xmgr, none
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96       -d <enum> (z)
97              Direction of the normal on the membrane: z, x, y
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99       -sl <int> (1)
100              Calculate  order  parameter  as function of box length, dividing
101              the box into this number of slices.
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103       -[no]szonly (no)
104              Only give Sz element of order tensor.  (axis  can  be  specified
105              with -d)
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107       -[no]unsat (no)
108              Calculate  order  parameters  for unsaturated carbons. Note that
109              this cannot be mixed with normal order parameters.
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111       -[no]permolecule (no)
112              Compute per-molecule Scd order parameters
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114       -[no]radial (no)
115              Compute a radial membrane normal
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117       -[no]calcdist (no)
118              Compute distance from a reference
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SEE ALSO

121       gmx(1)
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123       More    information    about    GROMACS    is    available    at     <‐
124       http://www.gromacs.org/>.
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127       2020, GROMACS development team
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1322019.6                           Feb 28, 2020                     GMX-ORDER(1)
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