where 𝑠 𝑖𝑗 = 1 if the contacts between the atoms i and j is formed between the independent stem units of RNA. f. angvec. The angvec collective variable is defined as the angle between two vectors 𝑏 ⃗ and 𝑑 , where 𝑏 ⃗ is defined as the vector connecting center of mass of backbone and sugar region of residues 9, 10, 11, and 12 towards residues 1,2,3 and 4. 𝑑 is defined as the vector connecting a nitrogen atom of the Guanidium end and the oxygen group of the c-alpha end of Arginine.