g_sgangle - computes the angle and distance between two groups
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
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
-s topol.tpr Input
Run input file: tpr tpb tpa
-oa sg_angle.xvg Output
-od sg_dist.xvg Output, Opt.
-od1 sg_dist1.xvg Output, Opt.
-od2 sg_dist2.xvg Output, Opt.
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
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)