NAME

       g_sgangle - computes the angle and distance between two groups

       VERSION 4.6.5

SYNOPSIS

       g_sgangle  -f  traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2
       sg_dist2.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]one -[no]z

DESCRIPTION

       Compute the angle and distance between two groups.  The groups are defined by a number of atoms given  in
       an index file and may be two or three atoms in size.  If  -one is set, only one group should be specified
       in  the  index  file  and  the  angle  between  this  group at time 0 and t will be computed.  The angles
       calculated depend on the order in which the atoms are given. Giving, for instance, 5 6  will  rotate  the
       vector 5-6 with 180 degrees compared to giving 6 5.

       If  three atoms are given, the normal on the plane spanned by those three atoms will be calculated, using
       the formula  P1P2 x P1P3.  The cos of the angle is calculated, using the inproduct of the two  normalized
       vectors.

       Here is what some of the file options do:

         -oa:  Angle  between  the  two  groups specified in the index file. If a group contains three atoms the
       normal to the plane defined by those three atoms will be used. If a group contains two atoms, the  vector
       defined by those two atoms will be used.

         -od:  Distance  between two groups. Distance is taken from the center of one group to the center of the
       other group.

        -od1: If one plane and one vector is given, the distances for each of the atoms from the center  of  the
       plane is given separately.

        -od2: For two planes this option has no meaning.

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

       -oa sg_angle.xvg Output
        xvgr/xmgr file

       -od sg_dist.xvg Output, Opt.
        xvgr/xmgr file

       -od1 sg_dist1.xvg Output, Opt.
        xvgr/xmgr file

       -od2 sg_dist2.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

       -[no]oneno
        Only one group compute angle between vector at time zero and time t

       -[no]zno
        Use the  z-axis as reference

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                     g_sgangle(1)