Provided by: gromacs-data_4.6.5-1build1_all bug


       g_sgangle - computes the angle and distance between two groups

       VERSION 4.6.5


       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


       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.


       -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


        Print help info and quit

        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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

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

        Only one group compute angle between vector at time zero and time t

        Use the  z-axis as reference



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                             g_sgangle(1)