ArticleIBM journal of research and development
Scalable Molecular Dynamics with NAMD on the Summit System.
Article in IBM journal of research and development. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Atomistic Simulations of Sarcomere Proteins.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics.The journal of physical chemistry. B · 2023Article
- Application Experiences on a GPU-Accelerated Arm-based HPC Testbed.The proceedings of International Conference on High Performance Computing in Asia-Pacific Region (HPC Asia 2023 Workshops) : 27 February to 2 March 2023, Singapore. International Conference/Exhibition on High-Performance Computing in th... · 2023Article
- An Integrated Mass Spectrometry-Based Glycomics-Driven Glycoproteomics Analytical Platform to Functionally Characterize Glycosylation Inhibitors.Molecules (Basel, Switzerland) · 2022Article
- Biophysical Insight into the SARS-CoV2 Spike-ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational Approach.ACS omega · 2022Article
- Combined 3D-QSAR, molecular docking and dynamics simulations studies to model and design TTK inhibitors.Frontiers in chemistry · 2022Article
- Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites.Frontiers in molecular biosciences · 2022Article
- AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.The international journal of high performance computing applications · 2021Article
- Itraconazole inhibits nuclear delivery of extracellular vesicle cargo by disrupting the entry of late endosomes into the nucleoplasmic reticulum.Journal of extracellular vesicles · 2021Article
- Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach.Journal of molecular modeling · 2021Article
- Biomolecular modeling thrives in the age of technology.Nature computational science · 2021Article
- Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase.Nature communications · 2021Article
- Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions.The journal of physical chemistry. B · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and dynamics of large biomolecular complexes, such as viruses like HIV and various types of influenza. State-of-the-art biomolecular simulations often require integration of billions of timesteps, computing all interatomic forces for each femtosecond timestep. Molecular dynamics simulation of large biomolecular systems and long-timescale biological phenomena requires tremendous computing power. NAMD harnesses the power of thousands of heterogeneous processors to meet this demand. In this paper, we present algorithm improvements and performance optimizations that enable NAMD to achieve high performance on the IBM Newell platform (with POWER9 processors and NVIDIA Volta V100 GPUs) which underpins the Oak Ridge National Laboratory's Summit and Lawrence Livermore National Laboratory's Sierra supercomputers. The Top-500 supercomputers June 2018 list shows Summit at the number one spot with 187 Petaflop/s peak performance and Sierra third with 119 Petaflop/s. Optimizations for NAMD on Summit include: data layout changes for GPU acceleration and CPU vectorization, improving GPU offload efficiency, increasing performance with PAMI support in Charm++, improving efficiency of FFT calculations, improving load balancing, enabling better CPU vectorization and cache performance, and providing an alternative thermostat through stochastic velocity rescaling. We also present performance scaling results on early Newell systems.
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.