SoftwareX· 2015Q2
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
- 27,148citations
- Q2SCImago
- 2015year
Short summary
GROMACS version 5 achieves new performance heights in molecular simulations by implementing multi-level parallelization algorithms across SIMD, multithreading, CPU-GPU acceleration, domain decomposition, and ensemble-level parallelism.
AI-generated from the title and abstract; the full text is not read.
Key points
- GROMACS version 5 introduces advanced parallelization across SIMD, multithreading, and CPU-GPU acceleration.
- State-of-the-art 3D domain decomposition and ensemble-level parallelization (replica exchange, Copernicus) are integrated.
- The software supports a rich set of calculation types and advanced free-energy calculations.
- It now includes the latest compressed trajectory storage format for efficient data handling.
AI-generated from the title and abstract; the full text is not read.
Abstract
GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.
The authors' abstract, as published at the source. SoftwareX, 2015 · DOI ↗
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Field: Spectroscopy
SpectroscopyChemistry