NAME¶

g_sgangle - computes the angle and distance between two groups VERSION 4.5.4-dev-20110404-bc5695c

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 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[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 separately. -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 -[no]versionno
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) -[no]wno
View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -[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/>.