ArticleJournal of chemical theory and computation2023
Efficient Empirical Valence Bond Simulations with GROMACS.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Electrochemical Electron Transfer: Key Concepts, Theories, and Parameterization via Atomistic Simulations.Chemical reviews · 2026Review
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- Mechanistic Insights into the Ferroptosis-Regulating Effects of EF in the Treatment of Chronic Renal Failure.Current medicinal chemistry · 2026Article
- l-DOPA-Containing Protein Autoxidation: An Empirical Valence Bond Simulation of the Rate-Limiting Step.The journal of physical chemistry. B · 2025Article
- Toward Improving Multiple Time Step QM/MM Simulations with Δ-Machine Learning.The journal of physical chemistry. B · 2025Article
- Rescaling of Point Charges as a Way to Improve the Simple-to-Use Electrostatic Embedding Scheme Developed to Explore Enzyme Activity with QM-Oriented Software.Journal of chemical information and modeling · 2025Article
- VeloxChem Quantum-Classical Interoperability for Modeling of Complex Molecular Systems.The journal of physical chemistry. A · 2025Article
- Decoding Enzymatic Dechlorination with Multiscale Modeling: Mechanistic Insights into Native Haloalkane Dehalogenase fromACS catalysis · 2025Article
- Identification of 2,3-oxidosqualene cyclase gene inHorticulture research · 2025Article
- Investigation of Electrostatic Effects on Enyzme Catalysis: Insights from Computational Simulations of Monoamine Oxidase A Pathological Variants Leading to the Brunner Syndrome.Journal of chemical information and modeling · 2025Article
- Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics.JACS Au · 2025Article
- Machine learning-based transcriptmics analysis revealsFrontiers in pharmacology · 2025Article
- Computational Insights into SARS-CoV-2 Main Protease Mutations and Nirmatrelvir Efficacy: The Effects of P132H and P132H-A173V.Journal of chemical information and modeling · 2024Article
- Molecular dynamic investigation for Roco4 kinase inhibitor as treatment options for parkinsonism.Journal of molecular modeling · 2024Article
- Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?Journal of chemical theory and computation · 2024Article
- Parishin B blocking TRIB3-AKT1 interaction inhibits breast cancer lung metastasis.Frontiers in pharmacology · 2024Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a protocol to perform empirical valence bond (EVB) simulations using GROMACS software. EVB is a fast and reliable method that allows one to determine the reaction free-energy profiles in complex systems, such as enzymes, by employing classical force fields to represent a chemical reaction. Therefore, running EVB simulations is basically as fast as any classical molecular dynamics simulation, and the method uses standard free-energy calculations to map the free-energy change along a given reaction path. To exemplify and validate our EVB implementation, we replicated two cases of our earlier enzyme simulations. One of these addresses the decomposition of the activation free energy into its enthalpic and entropic components, and the other is focused on calculating the overall catalytic effect of the enzyme compared to the same reaction in water. These two examples give virtually identical results to those obtained with programs that were specifically designed for EVB simulations and show that the GROMACS implementation is robust and can be used for very large systems.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.