ArticleJournal of computational chemistry2016
Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.The Journal of chemical physics · 2023Article
- CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.The journal of physical chemistry. B · 2022Article
- A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0].Living journal of computational molecular science · 2022Article
- Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.Journal of computational chemistry · 2020Article
- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti-Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide.International journal of molecular sciences · 2019Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates.Glycobiology · 2019Article
- Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.The journal of physical chemistry. B · 2018Article
- Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.Journal of chemical theory and computation · 2017Article
- Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.Bioinformatics (Oxford, England) · 2017Article
- Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time.The Journal of biological chemistry · 2017Article
- CHARMM-GUI 10 years for biomolecular modeling and simulation.Journal of computational chemistry · 2017Review
- Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.Journal of molecular graphics & modelling · 2017Article
- Efficient implementation of constant pH molecular dynamics on modern graphics processors.Journal of computational chemistry · 2016Article
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Authors and funding
2 authors.
Funding
Abstract
Two fundamental challenges of simulating biologically relevant systems are the rapid calculation of the energy of solvation and the trajectory length of a given simulation. The Generalized Born model with a Simple sWitching function (GBSW) addresses these issues by using an efficient approximation of Poisson-Boltzmann (PB) theory to calculate each solute atom's free energy of solvation, the gradient of this potential, and the subsequent forces of solvation without the need for explicit solvent molecules. This study presents a parallel refactoring of the original GBSW algorithm and its implementation on newly available, low cost graphics chips with thousands of processing cores. Depending on the system size and nonbonded force cutoffs, the new GBSW algorithm offers speed increases of between one and two orders of magnitude over previous implementations while maintaining similar levels of accuracy. We find that much of the algorithm scales linearly with an increase of system size, which makes this water model cost effective for solvating large systems. Additionally, we utilize our GPU-accelerated GBSW model to fold the model system chignolin, and in doing so we demonstrate that these speed enhancements now make accessible folding studies of peptides and potentially small proteins.
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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.