Biomolecular Simulation: A Perspective from High Performance Computing. Issue 7 (25th May 2020)

• Record Type: Journal Article
• Authors: Bolnykh, Viacheslav; Rothlisberger, Ursula; Carloni, Paolo
• Is Part Of: Israel journal of chemistry. Volume 60:Issue 7(2020)
• Page Start: 694
• Page End: 704
• Publication Date: 2020-05-25
• Subjects: Density Functional Theory -- Molecular Mechanics -- QM/MM -- Molecular Dynamics -- Massively parallel biomolecular simulations; Chemistry -- Periodicals; 540.5
• DOI: 10.1002/ijch.202000022
• Languages: English
• ISSNs: 0021-2148

Abstract

Abstract: High‐Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi‐threading and distributed computing) used in all the natural sciences, including molecular biophysics. Next, we describe how these strategies are applied in molecular dynamics simulations and enhanced sampling methods, either based on force fields, on density functional theory or on QM/MM potentials. As test cases, we focus on the widely used CPMD and GROMACS packages, along with a hybrid QM/MM interface coupling the two recently developed by a European team including the Authors. The review closes with a short perspective on the use of HPC‐based biomolecular simulations. Additional information on optimizations and software adjustments to maximize code performance are provided in the Supporting Information. Abstract :