In summary we find MD-approaches, including NES, can resolve the pK a values of cysteine and histidine residues with accuracy that exceeds conventional methods; however, this requires modification to the underlying MD force fields. The largest accuracy improvement we observed was for charge scaling the CHARMM36m force field, a result that will likely extend to other force fields and could remedy the poorer accuracy previously observed for predicting the effect of charge-changing mutations on protein thermostability and binding affinity. More work will help determine the consequences of charge-scaling; however, this work and the recent work of others seems to suggest that charge-scaling may be a general method to enhance the accuracy of non-polarizable MM force fields with only minimal and predictable costs. 1.0 0.9 0.9 0.9 0.9 0.9 0.8 0. (b) Exploring the RDF RMSD matrix of (σ, ϵ) pairs reveals that changes to σ alter the value significantly more than changes in ϵ. For CHARMM36m, the default value of σ = 1.00 well reproduces the position of the first RDF peak calculated from ab initio molecular dynamics, while for Amber14SB a value of σ ≈ 1.10 is required. The (σ, ϵ) pair that minimizes the RMSD between the MD and AIMD RDF curves is indicated with a box. on σ when using OPC (green) or mTIP3P (blue). The difference is larger than that observed for using a smaller box (e.g. 30 Å). Slightly different solvation free energies are calculated for the default sulfur thiolate: σ = 1.00; however, both models would suggest an identical sulfur thiolate: