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NAME

       g_sgangle - computes the angle and distance between two groups

       VERSION 4.0.1

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

       -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

       -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

       -[no]xvgryes
        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -[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/>.

                                Thu 16 Oct 2008                   g_sgangle(1)