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.
|-f||traj.xtc||Input||Trajectory: xtc trr trj gro g96 pdb cpt|
|-s||topol.tpr||Input||Run input file: tpr tpb tpa|
|-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|
|-[no]h||gmx_bool||no||Print help info and quit|
|-[no]version||gmx_bool||no||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]w||gmx_bool||no||View output xvg, xpm, eps and pdb files|
|-xvg||enum||xmgrace||xvg plot formatting: xmgrace, xmgr or none|
|-[no]one||gmx_bool||no||Only one group compute angle between vector at time zero and time t|
|-[no]z||gmx_bool||no||Use the Z-axis as reference|