ArticleAnalytical chemistry2024
High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method.
Article in Analytical chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- A deep dive into ferritin nanoparticle advancements: experimental and computational perspectives.Discover nano · 2026Review
- Effect of emulsion-based nanosystems on the encapsulation behavior of triptorelin using molecular dynamics simulation.Journal of computer-aided molecular design · 2026Article
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation.Journal of chemical theory and computation · 2025Article
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4 authors.
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Abstract
Native mass spectrometry (MS) is widely employed to study the structures and assemblies of proteins ranging from small monomers to megadalton complexes. Molecular dynamics (MD) simulation is a useful complement as it provides the spatial detail that native MS cannot offer. However, MD simulations performed in the gas phase have suffered from rapidly increasing computational costs with the system size. The primary bottleneck is the calculation of electrostatic forces, which are effective over long distances and must be explicitly computed for each atom pair, precluding efficient use of methods traditionally used to accelerate condensed-phase simulations. As a result, MD simulations have been unable to match the capacity of MS in probing large multimeric protein complexes. Here, we apply the fast multipole method (FMM) for computing the electrostatic forces, recently implemented by Kohnke et al. (
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