g_sgangle VERSION 3.3_beta_20050823

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]pbc -[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 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.

-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb

-n index.ndx Input Index file

-s topol.tpr Input Generic run input: tpr tpb tpa xml

-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

-[no]h no 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]w no View output xvg, xpm, eps and pdb files

-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]pbc no Use periodic boundary conditions

-[no]one no Only one group compute angle between vector at time zero and time t

-[no]z no Use the Z-axis as reference

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.