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


gmx order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nr [<.ndx>]]
[-s [<.tpr>]] [-o [<.xvg>]] [-od [<.xvg>]] [-ob [<.pdb>]]
[-os [<.xvg>]] [-Sg [<.xvg>]] [-Sk [<.xvg>]]
[-Sgsl [<.xvg>]] [-Sksl [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-d <enum>] [-sl <int>]
[-[no]szonly] [-[no]unsat] [-[no]permolecule] [-[no]radial]


gmx order computes the order parameter per atom for carbon tails. For atom i the vector
i-1, i+1 is used together with an axis. The index file should contain only the groups to
be used for calculations, with each group of equivalent carbons along the relevant acyl
chain in its own group. There should not be any generic groups (like System, Protein) in
the index file to avoid confusing the program (this is not relevant to tetrahedral order
parameters however, which only work for water anyway).

gmx order can also give all diagonal elements of the order tensor and even calculate the
deuterium order parameter Scd (default). If the option -szonly is given, only one order
tensor component (specified by the -d option) is given and the order parameter per slice
is calculated as well. If -szonly is not selected, all diagonal elements and the deuterium
order parameter is given.

The tetrahedrality order parameters can be determined around an atom. Both angle an
distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys.,
93, (1998), 511-518. for more details.


Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-n [<.ndx>] (index.ndx)
Index file

-nr [<.ndx>] (index.ndx)
Index file

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

Options to specify output files:

-o [<.xvg>] (order.xvg)
xvgr/xmgr file

-od [<.xvg>] (deuter.xvg)
xvgr/xmgr file

-ob [<.pdb>] (eiwit.pdb)
Protein data bank file

-os [<.xvg>] (sliced.xvg)
xvgr/xmgr file

-Sg [<.xvg>] (sg-ang.xvg) (Optional)
xvgr/xmgr file

-Sk [<.xvg>] (sk-dist.xvg) (Optional)
xvgr/xmgr file

-Sgsl [<.xvg>] (sg-ang-slice.xvg) (Optional)
xvgr/xmgr file

-Sksl [<.xvg>] (sk-dist-slice.xvg) (Optional)
xvgr/xmgr file

Other options:

-b <time> (0)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-dt <time> (0)
Only use frame when t MOD dt = first time (ps)

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-d <enum> (z)
Direction of the normal on the membrane: z, x, y

-sl <int> (1)
Calculate order parameter as function of box length, dividing the box into this
number of slices.

-[no]szonly (no)
Only give Sz element of order tensor. (axis can be specified with -d)

-[no]unsat (no)
Calculate order parameters for unsaturated carbons. Note that this cannot be mixed
with normal order parameters.

-[no]permolecule (no)
Compute per-molecule Scd order parameters

-[no]radial (no)
Compute a radial membrane normal

-[no]calcdist (no)
Compute distance from a reference

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