ArticleJournal of computational chemistry2019
Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.
Article in Journal of computational chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Multiscale modeling primer: Focus on chromatin and epigenetics.The Journal of biological chemistry · 2026Review
- Computing complexity.Nature chemical biology · 2026Article
- Deep learning insights into β-lactamase dynamics and resistance evolution.The Biochemical journal · 2026Review
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- A parallel CUDA implementation of the Gauss-Legendre-spherical-t method for electrostatic interactions.The Journal of chemical physics · 2025Article
- Gauss-Legendre-spherical-t (GLST) cubature-based factorization of long-range electrostatics in simulations.The Journal of chemical physics · 2025Article
- VTX: real-time high-performance molecular structure and dynamics visualization software.Bioinformatics (Oxford, England) · 2025Article
- GPU Accelerated Hybrid Particle-Field Molecular Dynamics: Multi-Node/Multi-GPU Implementation and Large-Scale Benchmarks of the OCCAM Code.Journal of computational chemistry · 2025Article
- High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM.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
- Enabling Atomistic Modeling and Simulation of Complex Curved Cellular Membranes with xMAS Builder.bioRxiv : the preprint server for biology · 2025Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model.Frontiers in bioinformatics · 2025Article
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Structure prediction of alternative protein conformations.Nature communications · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.Nature communications · 2024Article
- Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor.European biophysics journal : EBJ · 2024Article
- LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways.Journal of chemical information and modeling · 2023Article
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14 authors.
Funding
Abstract
The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a large number of atoms interacting through complex forcefields. To address this, we developed and implemented strategies in the GENESIS molecular dynamics package designed for large numbers of processors. Long-range electrostatic interactions were parallelized by minimizing the number of processes involved in communication. A novel algorithm was implemented for nonbonded interactions to increase single instruction multiple data (SIMD) performance, reducing memory usage for ultra large systems. Memory usage for neighbor searches in real-space nonbonded interactions was reduced by approximately 80%, leading to significant speedup. Using experimental data describing physical 3D chromatin interactions, we constructed the first atomistic model of an entire gene locus (GATA4). Taken together, these developments enabled the first billion-atom simulation of an intact biomolecular complex, achieving scaling to 65,000 processes (130,000 processor cores) with 1 ns/day performance. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.
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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.