g_sgangle_d (1) - Linux Manuals

g_sgangle_d: computes the angle and distance between two groups


g_sgangle - computes the angle and distance between two groups



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


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
 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 


 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)

 View output xvg, xpm, eps and pdb files

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

 Only one group compute angle between vector at time zero and time t

 Use the Z-axis as reference



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