ArticleJournal of computational chemistry2020
Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.
Article in Journal of computational chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Bone Healing via Carvacrol and Curcumin Nanoparticle on 3D Printed Scaffolds.Small (Weinheim an der Bergstrasse, Germany) · 2024Article
- Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.Journal of chemical theory and computation · 2024Article
- Article
- Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation.Journal of the American Chemical Society · 2024Article
- Application of Hierarchical Clustering to Analyze Solvent-Accessible Surface Area Patterns inBiology · 2022Article
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- TMPRSS2 inhibitor discovery facilitated through anbioRxiv : the preprint server for biology · 2021Article
- Targeting Intrinsically Disordered Proteins through Dynamic Interactions.Biomolecules · 2020Review
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Authors and funding
7 authors.
Funding
Abstract
The generalized Born with molecular volume and solvent accessible surface area (GBMV2/SA) implicit solvent model provides an accurate description of molecular volume and has the potential to accurately describe the conformational equilibria of structured and disordered proteins. However, its broader application has been limited by the computational cost and poor scaling in parallel computing. Here, we report an efficient implementation of both the electrostatic and nonpolar components of GBMV2/SA on graphics processing unit (GPU) within the CHARMM/OpenMM module. The GPU-GBMV2/SA is numerically equivalent to the original CPU-GBMV2/SA. The GPU acceleration offers ~60- to 70-fold speedup on a single NVIDIA TITAN X (Pascal) graphics card for molecular dynamic simulations of both folded and unstructured proteins of various sizes. The current implementation can be further optimized to achieve even greater acceleration with minimal reduction on the numerical accuracy. The successful development of GPU-GBMV2/SA greatly facilitates its application to biomolecular simulations and paves the way for further development of the implicit solvent methodology. © 2019 Wiley Periodicals, Inc.
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