ArticleThe journal of physical chemistry. B2012
Exploring, refining, and validating the paradynamics QM/MM sampling.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Benchmark of Approximate Quantum Chemical and Machine Learning Potentials for Biochemical Proton Transfer Reactions.Journal of chemical theory and computation · 2025Article
- A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS.Journal of computational chemistry · 2025Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods.Journal of chemical theory and computation · 2019Article
- Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level.Molecules (Basel, Switzerland) · 2018Article
- A comparison of X-ray and calculated structures of the enzyme MTH1.Journal of molecular modeling · 2016Article
- Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.Journal of computational chemistry · 2016Article
- Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.Journal of chemical theory and computation · 2016Article
- Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.The Journal of chemical physics · 2016Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions.The journal of physical chemistry. B · 2016Article
- Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method.Methods in enzymology · 2016Article
- Recent advances in QM/MM free energy calculations using reference potentials.Biochimica et biophysica acta · 2015Review
- On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations.The journal of physical chemistry. B · 2015Article
- Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters.The journal of physical chemistry. B · 2014Article
- Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).Angewandte Chemie (International ed. in English) · 2014Article
- Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model.Journal of chemical theory and computation · 2014Article
- Computer aided enzyme design and catalytic concepts.Current opinion in chemical biology · 2014Review
- An effective coarse-grained model for biological simulations: recent refinements and validations.Proteins · 2014Article
- Quantitative exploration of the molecular origin of the activation of GTPase.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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2 authors.
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Abstract
The performance of the paradynamics (PD) reference potential approach in QM/MM calculations is examined. It is also clarified that, in contrast to some possible misunderstandings, this approach provides a rigorous strategy for QM/MM free energy calculations. In particular, the PD approach provides a gradual and controlled way of improving the evaluation of the free energy perturbation associated with moving from the EVB reference potential to the target QM/MM surface. This is achieved by moving from the linear response approximation to the full free energy perturbation approach in evaluating the free energy changes. We also present a systematic way of improving the reference potential by using Gaussian-based correction potentials along a reaction coordinate. In parallel, we review other recent adaptations of the reference potential approach, emphasizing and demonstrating the advantage of using the EVB potential as a reference potential, relative to semiempirical QM/MM molecular orbital potentials. We also compare the PD results to those obtained by direct calculations of the potentials of the mean force (PMF). Additionally, we propose a way of accelerating the PMF calculations by using Gaussian-based negative potentials along the reaction coordinate (which are also used in the PD refinement). Finally, we discuss performance of the PD and the metadynamics approaches in ab initio QM/MM calculations and emphasize the advantage of using the PD approach.
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