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

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

SYNOPSIS
	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]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, 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  op-
     tion)  is given and the order parameter per slice is calculated as well. If
     -szonly is not selected, all diagonal elements and the deuterium order  pa-
     rameter 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 files:

     -f [<.xtc/.trr/...>] (traj.xtc)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

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

     -nr [<.ndx>] (index.ndx) (Optional)
	    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) (Optional)
	    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)
	    Time of first frame to read from trajectory (default unit ps)

     -e <time> (0)
	    Time of last frame to read from trajectory (default unit ps)

     -dt <time> (0)
	    Only use frame when t MOD dt = first time (default unit 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]permolecule (no)
	    Compute per-molecule Scd order parameters

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

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

KNOWN ISSUES
     * This  tool only works for saturated carbons and united atom force fields.
       For anything else, it is highly recommended to use a  different	analysis
       method!

     * The option -unsat claimed to do analysis for unsaturated carbons but this
       hasn't worked ever since it was added and has thus been removed.

SEE ALSO
     gmx(1)

     More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			    GMX-ORDER(1)
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