ArticleComputer physics communications2015
Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.
Article in Computer physics communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping.Journal of chemical information and modeling · 2025Article
- Potential distribution theory of alchemical transfer.The Journal of chemical physics · 2025Article
- Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations.The journal of physical chemistry. B · 2024Article
- Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability.Journal of chemical theory and computation · 2024Article
- Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials.Journal of chemical information and modeling · 2024Article
- What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.Journal of chemical theory and computation · 2024Article
- Article
- Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series.Journal of chemical information and modeling · 2023Article
- Advances in the OCEAN-3 spectroscopy package.Physical chemistry chemical physics : PCCP · 2022Review
- Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge.Journal of computer-aided molecular design · 2022Article
- Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors.The Journal of chemical physics · 2020Article
- Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.Journal of chemical information and modeling · 2019Article
- Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes.PloS one · 2019Article
- Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials.Journal of chemical information and modeling · 2018Article
- Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes.Frontiers in molecular biosciences · 2018Article
- Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins.Journal of computational chemistry · 2017Article
- A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.Journal of computer-aided molecular design · 2017Article
- Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.ACS omega · 2016Article
- Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.The Journal of chemical physics · 2016Article
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Authors and funding
7 authors.
Funding
Abstract
Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.
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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.