ArticleJournal of chemical theory and computation2024
Guidelines for Free-Energy Calculations Involving Charge Changes.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Driving Forces of UCST and LCST Liquid-Liquid Phase Separations.ACS omega · 2026Article
- Toward Relative Redox Potential Predictions in Flavoproteins: Treatment of a Charge-Changing Mutation in Alchemical Free Energy Simulations.Journal of chemical theory and computation · 2026Article
- Predicting Solvation Free Energies of Molecules and Ions via First-Principles and Machine-Learning Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- MgJournal of the American Chemical Society · 2026Article
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- Immunoinformatics approach to engineer a multi-epitope vaccine against SdrG in skin commensal Staphylococcus epidermidis.PloS one · 2026Article
- Computational Pipeline for Accelerating the Design of Glycomimetics.Journal of chemical information and modeling · 2025Article
- Benchmarking Alchemical Relative Binding Free Energy Calculations for Nucleotide Binding to Multimeric ATPases.Journal of chemical theory and computation · 2025Article
- Thermophobic diffusion becomes dominant in ultra-dilute alkali halide aqueous solutions.Communications chemistry · 2025Article
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- Probing Limitations of Co-Alchemical Charge Changes in Free-Energy Calculations.Journal of chemical theory and computation · 2025Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.Nucleic acids research · 2025Article
- Absolute and Relative Binding Free Energy Calculations of Nucleotides to Multiple Protein Classes.Journal of chemical theory and computation · 2025Article
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations.Journal of chemical information and modeling · 2025Article
- Mutagenesis-based optimal design of plant peptide phytosulfokine for enhanced biological activity.Computational and structural biotechnology journal · 2025Article
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations.Journal of chemical theory and computation · 2024Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The Coulomb interactions in molecular simulations are inherently approximated due to the finite size of the molecular box sizes amenable to current-day compute power. Several methods exist for treating long-range electrostatic interactions, yet these approaches are subject to various finite-size-related artifacts. Lattice-sum methods are frequently used to approximate long-range interactions; however, these approaches also suffer from artifacts which become particularly pronounced for free-energy calculations that involve charge changes. The artifacts, however, also affect the sampling when plain simulations are performed, leading to a biased ensemble. Here, we investigate two previously described model systems to determine if artifacts continue to play a role when overall neutral boxes are considered, in the context of both free-energy calculations and sampling. We find that ensuring that no net-charge changes take place, while maintaining a neutral simulation box, may be sufficient provided that the simulation boxes are large enough. Addition of salt to the solution (when appropriate) can further alleviate the remaining artifacts in the sampling or the calculated free-energy differences. We provide practical guidelines to avoid finite-size artifacts.
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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.