Recent advances in QM/MM free energy calculations using reference potentials

• Published in: Biochimica et biophysica acta Vol. 1850; no. 5; pp. 954 - 965
• Main Authors: Duarte, Fernanda, Amrein, Beat A., Blaha-Nelson, David, Kamerlin, Shina C.L.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2015; Elsevier Pub. Co
• Subjects: Averaging potential; Chlorides - chemistry; cost effectiveness; Energy Transfer; Ethylene Dichlorides - chemistry; Gibbs free energy; Hydrolases - chemistry; Kinetics; Mean field approximation; Methyl Chloride - chemistry; molecular dynamics; Molecular Dynamics Simulation - standards; Multiscale modeling; Protein Conformation; Protein Folding; Protein Stability; Protein Unfolding; Proteins - chemistry; QM/MM free energy calculation; Reference potential; Reference Standards; Review; Structure-Activity Relationship; Surface Properties; Thermodynamics; Uracil - chemistry; RS; Mean field approximation; CG; ABF; PMF; QM/MM; REMD; Multiscale modeling; EVB; FEP; PD; QTCP; MD; Reference potential; LRA; Averaging potential; SCC-DFTB; QM/MM free energy calculation; US; TS

Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meani...