Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.

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 uns

SUBMITTER: Gong X 

PROVIDER: S-EPMC7076882 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature