ArticleJournal of chemical theory and computation2021
Dummy Atoms in Alchemical Free Energy Calculations.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- 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
- One Blob to Rule Them All: A Universal Dual-Topology Nonequilibrium Framework for Relative and Absolute Binding Free Energies via a Lennard-Jones Blob Reference.Journal of chemical theory and computation · 2026Article
- Dual-Coordinate Relative Free Energy Simulations Using Machine-Learned Interatomic Potentials.Journal of chemical theory and computation · 2026Article
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal 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
- Architecture-Independent Absolute Solvation Free Energy Calculations with Neural Network Potentials.The journal of physical chemistry letters · 2025Article
- Accurate predictions of protein mutational effects accelerated with a hybrid-topology free energy protocol.Communications chemistry · 2025Article
- Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping.Journal of chemical information and modeling · 2025Article
- Manipulating Electronic Effect of Nitrogen Donor-Based Ligands for Efficient Complexation and Separation of Palladium from Highly Acidic Solution.Molecules (Basel, Switzerland) · 2025Article
- IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates.The journal of physical chemistry. B · 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
- Multiple Topology Replica Exchange of Expanded Ensembles for Multidimensional Alchemical Calculations.Journal of chemical theory and computation · 2025Article
- Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.Journal of chemical information and modeling · 2024Article
- Alchemical Enhanced Sampling with Optimized Phase Space Overlap.Journal of chemical theory and computation · 2024Article
- Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations.Journal of chemical theory and computation · 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
- Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.Journal of chemical theory and computation · 2023Article
- Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field.Journal of chemical theory and computation · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
In calculations of relative free energy differences, the number of atoms of the initial and final states is rarely the same. This necessitates the introduction of dummy atoms. These placeholders interact with the physical system only by bonded energy terms. We investigate the conditions necessary so that the presence of dummy atoms does not influence the result of a relative free energy calculation. On the one hand, one has to ensure that dummy atoms only give a multiplicative contribution to the partition function so that their contribution cancels from double-free energy differences. On the other hand, the bonded terms used to attach a dummy atom (or group of dummy atoms) to the physical system have to maintain it in a well-defined position and orientation relative to the physical system. A detailed theoretical analysis of both aspects is provided, illustrated by 24 calculations of relative solvation free energy differences, for which all four legs of the underlying thermodynamic cycle were computed. Cycle closure (or lack thereof) was used as a sensitive indicator to probing the effects of dummy atom treatment on the resulting free energy differences. We find that a naive (but often practiced) treatment of dummy atoms results in errors of up to
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