ArticleJournal of chemical theory and computation2018
Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- From Enhanced Sampling to Human-Readable Representations of Protein Dynamics.Journal of chemical theory and computation · 2026Article
- Transformer-accelerated discovery of inhibitors targeting the RpsAJournal of cheminformatics · 2026Article
- Fast sampling of protein conformational dynamics.Science advances · 2026Article
- Nanobody engineering: computational modelling and design for biomedical and therapeutic applications.FEBS open bio · 2025Review
- Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1.0].Living journal of computational molecular science · 2025Article
- Characterization of Posttranslationally Modified PHF-1 Tau Peptides Using Gaussian Accelerated Molecular Dynamics Simulation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling.Journal of chemical theory and computation · 2023Article
- Gaussian Accelerated Molecular Dynamics in OpenMM.The journal of physical chemistry. B · 2022Article
- GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling.Journal of chemical theory and computation · 2022Article
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs.Advances in protein chemistry and structural biology · 2022Review
- Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor.Computational and structural biotechnology journal · 2022Article
- Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.Journal of chemical theory and computation · 2021Article
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Mechanism of Ligand Recognition by Human ACE2 Receptor.The journal of physical chemistry letters · 2021Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Mechanism of ligand recognition by human ACE2 receptor.bioRxiv : the preprint server for biology · 2020Article
- Application of a Distance-Dependent Sigmoidal Dielectric Constant to the REMC/SAAP3D Simulations of Chignolin, Trp-Cage, and the G10q Mutant.The protein journal · 2020Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem.International journal of molecular sciences · 2019Article
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3 authors.
Funding
Abstract
Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.
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