GROMACS version:2020/23
GROMACS modification: No
Can’t find how to configure gmx gangle properly (google suggests this is confusing to many)
Following from manual:
If -g1 is vector or plane , -group1 should specify selections that contain either pairs (vector ) or triplets (plane ) of positions. For vectors, the positions set the endpoints of the vector, and for planes, the three positions are used to calculate the normal of the plane. In both cases, -g2 specifies the other vector to use (see below).
How to specify pairs and triplets in the ndx file? Is there a special format for this. I can’t find the format anywhere - brackets of pairs or something?
At the moment, I have just combined groups for the two end points of the vectors into one group. I don’t know if this is right as it seems this group is just a bunch of coordinates and vector ends are not defined.