ArticleJournal of computational chemistry2022
Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.
Article in Journal of computational chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods.The Journal of chemical physics · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.The journal of physical chemistry. B · 2024Article
- Updates to Protex for Simulating Proton Transfers in an Ionic Liquid.The journal of physical chemistry. B · 2024Article
- Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- 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
- Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach.Journal of chemical theory and computation · 2023Article
- Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.Journal of computational chemistry · 2022Article
- Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool.Frontiers in molecular biosciences · 2022Article
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Authors and funding
4 authors.
Funding
Abstract
We describe the theory of the so-called common-core/serial-atom-insertion (CC/SAI) approach to compute alchemical free energy differences and its practical implementation in a Python package called Transformato. CC/SAI is not tied to a specific biomolecular simulation program and does not rely on special purpose code for alchemical transformations. To calculate the alchemical free energy difference between several small molecules, the physical end-states are mutated into a suitable common core. Since this only requires turning off interactions, the setup of intermediate states is straightforward to automate. Transformato currently supports CHARMM and OpenMM as back ends to carry out the necessary molecular dynamics simulations, as well as post-processing calculations. We validate the method by computing a series of relative solvation free energy differences.
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