ArticleJournal of chemical theory and computation2020
Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed.
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Conformational dynamics underlying atypical chemokine receptor 3 activation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.Journal of chemical theory and computation · 2023Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models.Journal of chemical information and modeling · 2023Article
- Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations.Journal of chemical theory and computation · 2023Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Temperature replica exchange molecular dynamics (REMD) is a widely used enhanced sampling method for accelerating biomolecular simulations. During the past 2 decades, several variants of REMD have been developed to further improve the rate of conformational sampling of REMD. One such variant, reservoir REMD (RREMD), was shown to improve the rate of conformational sampling by around 5-20×. Despite the significant increase in the sampling speed, RREMD methods have not been widely used because of the difficulties in building the reservoir and also because of the code not being available on the graphics processing units (GPUs). In this work, we ported the Amber RREMD code onto GPUs making it 20× faster than the central processing unit code. Then, we explored protocols for building Boltzmann-weighted reservoirs as well as non-Boltzmann reservoirs and tested how each choice affects the accuracy of the resulting RREMD simulations. We show that, using the recommended protocols outlined here, RREMD simulations can accurately reproduce Boltzmann-weighted ensembles obtained by much more expensive conventional temperature-based REMD simulations, with at least 15× faster convergence rates even for larger proteins (>50 amino acids) compared to conventional REMD.
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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.