ArticleJournal of chemical information and modeling2021
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics.
Article in Journal of chemical information and modeling, 2021. 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.
- Spin Relaxation Does Not Preclude Magnetic Field Effects on Lipid Autoxidation.ACS central science · 2026Article
- The interaction of small molecules with phospholipid membranes studied by solid-state NMR and molecular dynamics simulation.Biophysical reviews · 2025Review
- Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Evaluating Polarizable Biomembrane Simulations against Experiments.Journal of chemical theory and computation · 2024Article
- Efficient calculation of orientation-dependent lipid dynamics from membrane simulations.bioRxiv : the preprint server for biology · 2024Article
- Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations.Communications chemistry · 2024Article
- Overlay databank unlocks data-driven analyses of biomolecules for all.Nature communications · 2024Article
- Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions.Journal of chemical theory and computation · 2023Article
- Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics.Biophysical journal · 2023Article
- Article
- An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.Journal of chemical information and modeling · 2023Review
- Structure of POPC Lipid Bilayers in OPLS3e Force Field.Journal of chemical information and modeling · 2022Article
- A method to construct the dynamic landscape of a bio-membrane with experiment and simulation.Nature communications · 2022Article
- Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes.Biophysical journal · 2022Article
- CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids.Journal of chemical theory and computation · 2021Article
- Model-Free or Not?Frontiers in molecular biosciences · 2021Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin-lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of ∼1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope-not only for lipid membranes but for all biomacromolecular systems.
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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.