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)