# The collective variables. This file defines WHAT IS MEASURED; `umbrella.yaml` beside it says
# which of these are biased and how. One definition, read once, so the quantity that is restrained
# and the quantity that is reported cannot differ.
#
# Indices are 0-based into the built topology. They are explicit and never inferred: a CV series
# that names the wrong four atoms cannot be told apart from one that names the right four.
schema_version: 1
collective_variables:
  # Alanine dipeptide, as built from tests/data/ALA.pdb.
  - {name: phi_ALA, type: torsion, atom_indices: [4, 6, 8, 14]}
  - {name: psi_ALA, type: torsion, atom_indices: [6, 8, 14, 16]}