Main Table of Contents

Fri 5 Jul 2013


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
-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]h bool no Print help info and quit
-[no]version 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 bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]one bool no Only one group compute angle between vector at time zero and time t
-[no]z bool no Use the z-axis as reference