NAME

       g_order - computes the order parameter per atom for carbon tails

       VERSION 4.6.5

SYNOPSIS

       g_order -f traj.xtc -n index.ndx -nr index.ndx -s topol.tpr -o order.xvg -od deuter.xvg -ob eiwit.pdb -os
       sliced.xvg  -Sg  sg-ang.xvg  -Sk  sk-dist.xvg  -Sgsl  sg-ang-slice.xvg  -Sksl  sk-dist-slice.xvg   -[no]h
       -[no]version  -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

       Compute 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).

       The program 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.

FILES

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
        Index file

       -nr index.ndx Input
        Index file

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -o order.xvg Output
        xvgr/xmgr file

       -od deuter.xvg Output
        xvgr/xmgr file

       -ob eiwit.pdb Output
        Protein data bank file

       -os sliced.xvg Output
        xvgr/xmgr file

       -Sg sg-ang.xvg Output, Opt.
        xvgr/xmgr file

       -Sk sk-dist.xvg Output, Opt.
        xvgr/xmgr file

       -Sgsl sg-ang-slice.xvg Output, Opt.
        xvgr/xmgr file

       -Sksl sk-dist-slice.xvg Output, Opt.
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -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]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -d enum z
        Direction of the normal on the membrane:  z,  x or  y

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

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

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

       -[no]permoleculeno
        Compute per-molecule Scd order parameters

       -[no]radialno
        Compute a radial membrane normal

       -[no]calcdistno
        Compute distance from a reference

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                       g_order(1)