ArticleProtein science : a publication of the Protein Society2022
CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity.Nature communications · 2026Article
- A Quadrupolar Fullerene Model System for Benchmarking Enhanced Sampling of Trapped Waters in Free Energy Calculations.The journal of physical chemistry. B · 2026Article
- Characterization of Gas-Phase Native(-like) Proteins Using Structures for Lossless Ion Manipulations.Analytical chemistry · 2026Article
- Ligand-Binding Free Energy Simulations of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- Substrates (Acyl-CoA and Diacylglycerol) Entry and Products (CoA and Triacylglycerol) Egress Pathways in DGAT1.Journal of computational chemistry · 2025Article
- Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding.The journal of physical chemistry. B · 2025Article
- Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- The Putative Role ofInternational journal of molecular sciences · 2024Article
- Structural insights into the molecular recognition of integrin αVβ3 by RGD-containing ligands: The role of the specificity-determining loop (SDL).bioRxiv : the preprint server for biology · 2024Article
- Antiviral drug recognition and elevator-type transport motions of CNT3.Nature chemical biology · 2024Article
- CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation.Journal of molecular biology · 2024Article
- Analogs of α-conotoxin PnIC selectively inhibit α7β2- over α7-only subtype nicotinic acetylcholine receptors via a novel allosteric mechanism.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- CHARMM-GUIJournal of chemical theory and computation · 2023Review
- ExploitingFrontiers in genetics · 2023Article
- CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.Protein science : a publication of the Protein Society · 2022Article
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9 authors.
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Abstract
Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM-GUI Enhanced Sampler, a web-based tool to prepare various enhanced sampling simulations inputs with user-selected collective variables (CVs). Enhanced Sampler provides inputs for the following nine methods: accelerated MD, Gaussian accelerated MD, conformational flooding, metadynamics, adaptive biasing force, steered MD, temperature replica exchange MD, replica exchange solute tempering 2, and replica exchange umbrella sampling for the method-implemented MD packages including AMBER, CHARMM, GENESIS, GROMACS, NAMD, and OpenMM. Users only need to select a group of atoms via intuitive web-implementation in order to define commonly used nine CVs of interest: center of mass based distance, angle, dihedral, root-mean-square-distance, radius of gyration, distance projected on axis, two types of angles projected on axis, and coordination numbers. The enhanced sampling methods are tested with several biological systems to illustrate their efficiency over conventional MD. Enhanced Sampler with carefully optimized system-dependent parameters will help users to get meaningful results from their enhanced sampling simulations.
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