Publication

Biomolecular Simulation: a Perspective from High Performance Computing

Ursula Röthlisberger, Viacheslav Bolnykh, Paolo Carloni
2020
Journal Articles

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.

Official source

https://infoscience.epfl.ch/entities/publication/b8763966-a6ac-45b6-b12b-21827bfe4192

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Ursula Röthlisberger, Viacheslav Bolnykh, Paolo Carloni
2020
Journal Articles

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/b8763966-a6ac-45b6-b12b-21827bfe4192

About this result

Related concepts (23)

Force field (chemistry)

In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.

Supercomputer

A supercomputer is a computer with a high level of performance as compared to a general-purpose computer. The performance of a supercomputer is commonly measured in floating-point operations per second (FLOPS) instead of million instructions per second (MIPS). Since 2017, there have existed supercomputers which can perform over 1017 FLOPS (a hundred quadrillion FLOPS, 100 petaFLOPS or 100 PFLOPS). For comparison, a desktop computer has performance in the range of hundreds of gigaFLOPS (1011) to tens of teraFLOPS (1013).

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