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)