SBMOpenMM uses two files as input: a Protein Data Bank (PDB) format file for the protein structure and a contact file for specifying the native contact interactions (see Section SI I.A for detail on how to obtain this file). The topology and the set of bonded interactions are defined from the structure's connectivity. These include definitions of atoms participating in bonds, angles, and proper, improper, and planar torsions, together with their equilibrium distances. Likewise, nonbonded interactions are defined from the atomic pairs listed in the contact file, and their equilibrium distances are calculated from the input structure. This connectivity information, together with the set of force constant parameters, is used by the library to construct the relevant forces and system objects, directly employed by the OpenMM MD engine to start a simulation. The SBMOpenMM library contains methods to define the SBM force field composition and set default or custom models and parameters. To this end, the Python library is composed of three major classes (see also Figure ):