gmx-order(1) GROMACS Manual gmx-order(1)NAMEgmx-order - Compute the order parameter per atom for carbon tails
SYNOPSIS
gmx order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nr [<.ndx>]]
[-s [<.tpr/.tpb/...>]] [-o [<.xvg>]] [-od [<.xvg>]]
[-ob [<.pdb>]] [-os [<.xvg>]] [-Sg [<.xvg>]] [-Sk [<.xvg>]]
[-Sgsl [<.xvg>]] [-Sksl [<.xvg>]] [-nice <int>] [-b <time>]
[-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>] [-d <enum>]
[-sl <int>] [-[no]szonly] [-[no]unsat] [-[no]permolecule]
[-[no]radial] [-[no]calcdist]
DESCRIPTION
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, Pro‐
tein) 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 deu‐
terium 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
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input)
Index file
-nr [<.ndx>] (index.ndx) (Input)
Index file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-o [<.xvg>] (order.xvg) (Output)
xvgr/xmgr file
-od [<.xvg>] (deuter.xvg) (Output)
xvgr/xmgr file
-ob [<.pdb>] (eiwit.pdb) (Output)
Protein data bank file
-os [<.xvg>] (sliced.xvg) (Output)
xvgr/xmgr file
-Sg [<.xvg>] (sg-ang.xvg) (Output, Optional)
xvgr/xmgr file
-Sk [<.xvg>] (sk-dist.xvg) (Output, Optional)
xvgr/xmgr file
-Sgsl [<.xvg>] (sg-ang-slice.xvg) (Output, Optional)
xvgr/xmgr file
-Sksl [<.xvg>] (sk-dist-slice.xvg) (Output, Optional)
xvgr/xmgr file
Other options:
-nice <int> (19)
Set the nicelevel
-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> (xmgrace)
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
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-order(1)
