ArticleJournal of chemical information and modeling2024
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.
Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Atomic resolution structure of human papillomavirus bound to heparin.Nature communications · 2026Article
- 6-(2-Aminoethyl)-6Biomolecules · 2026Article
- A Coupled Refined Model of Atomistic and Continuum Parameters of Diatomic Covalent Bonds.Nanomaterials (Basel, Switzerland) · 2026Article
- AnCurrent drug targets · 2026Article
- Computational biophysical characterization of a superradiant virus-like particle in its ground state.bioRxiv : the preprint server for biology · 2025Article
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL.iScience · 2025Article
- All-atom MD simulations of the HPV16 capsid.bioRxiv : the preprint server for biology · 2025Article
- Developing T Cell Epitope-Based Vaccines Against Infection: Challenging but Worthwhile.Vaccines · 2025Review
- DNA damage and repair in the nucleosome: insights from computational methods.Biophysical reviews · 2024Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
All-atom molecular dynamics (MD) simulations are an essential structural biology technique with increasing application to multimillion-atom systems, including viruses and cellular machinery. Classical MD simulations rely on parameter sets, such as the AMBER family of force fields (AMBERff), to accurately describe molecular motion. Here, we present an implementation of AMBERff for use in NAMD that overcomes previous limitations to enable high-performance, massively parallel simulations encompassing up to two billion atoms. Single-point potential energy comparisons and case studies on model systems demonstrate that the implementation produces results that are as accurate as running AMBERff in its native engine.
Identifiers
What OpenQuestion holds
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.