NAME

       g_hydorder - computes tetrahedrality parameters around a given atom

       VERSION 4.6.5

SYNOPSIS

       g_hydorder  -f  traj.xtc  -n  index.ndx  -s  topol.tpr  -o  intf.xpm  -or  raw.out  -Spect
       intfspect.out -[no]h -[no]version -nice int -b time -e time -dt time -[no]w  -d  enum  -bw
       real -sgang1 real -sgang2 real -tblock int -nlevel int

DESCRIPTION

       g_hydorder computes the tetrahedrality order parameters around a given 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.  This application calculates the orderparameter in
       a 3d-mesh in the box, and with 2 phases in the box gives the user the option to  define  a
       2D interface in time separating the faces by specifying parameters -sgang1 and -sgang2 (It
       is important to select these judiciously)

FILES

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

       -n index.ndx Input
        Index file

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

       -o intf.xpm Output, Mult.
        X PixMap compatible matrix file

       -or raw.out Output, Opt., Mult.
        Generic output file

       -Spect intfspect.out Output, Opt., Mult.
        Generic output 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

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

       -bw real 1
        Binwidth of box mesh

       -sgang1 real 1
        tetrahedral angle parameter in Phase 1 (bulk)

       -sgang2 real 1
        tetrahedral angle parameter in Phase 2 (bulk)

       -tblock int 1
        Number of frames in one time-block average

       -nlevel int 100
        Number of Height levels in 2D - XPixMaps

SEE ALSO

       gromacs(7)

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

                                          Mon 2 Dec 2013                            g_hydorder(1)