Implementation and Validation of Titratable Cysteine in GROMACS-Based Constant-pH Molecular Dynamics

regime of these residues, while also showing that quantitative accuracy depends sensitively on the local conformational ensemble sampled around the introduced cysteine. Second, the implementation was applied to the reactive Cys106 of DJ-1, placing its titration in the correct acidic regime. Overall, this work establishes a practical cysteine extension of the GROMACS CpHMD framework for biomolecular simulations.