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• W2338036129 abstract "Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using “indirect” thermodynamic cycles to connect “low level” simulation results to “high level” free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔAMM→QM), as recently demonstrated by us and others, is differences in the so-called “stiff” degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski’s and Crooks’ equations. Initial applications of computing ΔANEWMM→QM, for blocked amino acids alanine and serine as well as to generate butane’s potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches." @default.
• W2338036129 created "2016-06-24" @default.
• W2338036129 creator A5037901921 @default.
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• W2338036129 date "2015-11-24" @default.
• W2338036129 modified "2023-10-14" @default.
• W2338036129 title "Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems" @default.
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• W2338036129 doi "https://doi.org/10.1021/acs.jpclett.5b02164" @default.
• W2338036129 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26539729" @default.
• W2338036129 hasPublicationYear "2015" @default.
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