ArticleJournal of computational chemistry2017
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
Article in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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57 citing papers in PubMed.
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- Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields.Journal of the American Chemical Society · 2024Article
- What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.Journal of chemical theory and computation · 2024Article
- Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy.International journal of molecular sciences · 2024Article
- Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects.Chemical science · 2023Article
- Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition.Journal of chemical information and modeling · 2023Article
- RNA-protein complexes and force field polarizability.Frontiers in chemistry · 2023Article
- Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with SmThe journal of physical chemistry. B · 2022Article
- Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model.The journal of physical chemistry. B · 2022Article
- Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions.Journal of chemical information and modeling · 2022Article
- Can electric fields drive chemistry for an aqueous microdroplet?Nature communications · 2022Article
- Polarizable Water Potential Derived from a Model Electron Density.Journal of chemical theory and computation · 2021Article
- Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes.Molecules (Basel, Switzerland) · 2021Article
- Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity.Accounts of chemical research · 2021Article
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8 authors.
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Abstract
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc.
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