Charge and Lennard-Jones parameters were derived from the QM ground state electron density using the DDEC scheme as implemented in the ONETEP code (Section 2.1). As discussed previously, DDEC charges show low, but non-zero, conformational dependence. To account for this, the non-bonded parameters were derived for multiple conformations of each dipeptide and averaged. Input files for the full set of dipeptide structures are provided in the Supporting Information. Non-bonded parameters on identical atoms (for example, hydrogen atoms in a methyl group) were symmetrized. It should be noted that only atom-centered charges were used in this work, though off-site charges to model anisotropic electron density distributions, particularly on sulfur atoms, may lead to improvements in future work. Bonded parameters were assigned to the dipeptides from the library developed using the modified Seminario method using OPLS-AA/M atom typing rules.