Best Practices in Constant pH MD Simulations: Accuracy and Sampling
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00517
Abstract: Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996,… read more here.
Keywords: force field; time scales; accuracy sampling; constant simulations ... See more keywords
Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pK(a) Calculations.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.6b00807
Abstract: Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable… read more here.
Keywords: chemically coupled; three states; states model; constant simulations ... See more keywords