Measuring Angles
Introduction
gmx gangle can be used to calculate the angles between groups of vectors. Specifically, gmx gangle can compute angles between a vector or plane and another vector, plane, the z-axis, or the normal vector of a sphere. It can also compute angles and dihedrals, similar to gmx angle.
Like the gmx distance command, this command allows us to study movement of features, like protein hinges.
Note
You will need to use a custom index file if you are measuring angles between custom groups of atoms.
You should have the following files:
- Trajectory files (.xtc)
- Topology file (.tpr)
- Index file (.ndx)
Using gmx gangle
To calculate angles:
gmx gangle -f trajectory.xtc -s topology.tpr -n index.ndx -tu ns -oav all-angles.xvg -oall all-angles.xvg -oh angle-hist.xvg -g1 vector -group1 <group> -g2 vector -group2 <group>
-g1 and -g2 indicate the type of angle that should be analyzed (vector, plane, angle, or dihedral). These options are closely tied to the -group1 and -group2 options, which specify the atom positions to be analyzed. The groups to be analyzed are taken from the index file supplied with -n.
As the inputs for these options are highly dependent on the system, refer to the gmx gangle documentation page for valid -g1/g2 and -group1/group2 combinations.
This produces the following outputs:
-oav: average angles as a function of time-oall: all angles as a function of time-oh: histogram of angles
These XVG files can be visualized using Python or Grace to produce a plots of angle versus time, or to generate a heat-map from histogram data.