Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units
| Autor: | Mara Chiricotto, Jianhan Chen, Charles L. Brooks, Michael Feig, Erik B. Nordquist, Xiping Gong, Xiaorong Liu |
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| Rok vydání: | 2019 |
| Předmět: |
Speedup
010304 chemical physics Computer science Surface Properties Graphics processing unit General Chemistry Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Article 0104 chemical sciences Computational science Accessible surface area Reduction (complexity) Computational Mathematics Acceleration Molecular dynamics 0103 physical sciences Computer Graphics Solvents Graphics Scaling |
| Zdroj: | J Comput Chem |
| ISSN: | 1096-987X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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