ArticleJournal of chemical theory and computation2013
Automated Optimization of Potential Parameters.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Reversible molecular simulation for training classical and machine-learning force fields.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Classical Models of Hydroxide for Proton Hopping Simulations.The journal of physical chemistry. B · 2024Article
- Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization.Journal of chemical theory and computation · 2023Article
- An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.Journal of chemical information and modeling · 2023Review
- Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set.Journal of chemical theory and computation · 2022Article
- Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting.Nature communications · 2021Article
- A Framework for Stochastic Optimization of Parameters for Integrative Modeling of Macromolecular Assemblies.Life (Basel, Switzerland) · 2021Article
- A Data-Driven Hydrophobicity Scale for Predicting Liquid-Liquid Phase Separation of Proteins.The journal of physical chemistry. B · 2021Article
- A Polarization-Consistent Model for Alcohols to Predict Solvation Free Energies.Journal of chemical information and modeling · 2020Article
- Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.Journal of computer-aided molecular design · 2019Review
- Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.Journal of chemical theory and computation · 2018Article
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins.Nature methods · 2017Article
- Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics.The journal of physical chemistry. B · 2015Article
- Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.The journal of physical chemistry. B · 2015Article
- United polarizable multipole water model for molecular mechanics simulation.The Journal of chemical physics · 2015Article
- Optimizing potentials for a liquid mixture: a new force field for a tert-butanol and water solution.The journal of physical chemistry. B · 2015Article
- Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.Methods in enzymology · 2015Article
- Building Force Fields: An Automatic, Systematic, and Reproducible Approach.The journal of physical chemistry letters · 2014Article
- One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery.Journal of chemical theory and computation · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
An algorithm and software to refine parameters of empirical energy functions according to condensed phase experimental measurements are discussed. The algorithm is based on sensitivity analysis and local minimization of the differences between experiment and simulation as a function of potential parameters. It is illustrated for a toy problem of alanine dipeptide and is applied to folding of the peptide WAAAH. The helix fraction is highly sensitive to the potential parameters while the slope of the melting curve is not. The sensitivity variations make it difficult to satisfy both observations simultaneously. We conjecture that there is no set of parameters that reproduces experimental melting curves of short peptides that are modeled with the usual functional form of a force field.
Identifiers
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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.