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       g_sgangle - computes the angle and distance between two groups

       VERSION 4.0.1


       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  -nice  int  -b
       time -e time -dt time -[no]w -[no]xvgr -[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 seperately.

       -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

       -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

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

        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

                                Thu 16 Oct 2008                   g_sgangle(1)