Hardening and Development of the GROMACS Molecular Simulation Engine

GROMACS 分子模拟引擎的强化和开发

• 批准号: 9266801
• 负责人: Peter M Kasson
• 金额: $ 26.4万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-05-01 至 2020-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9266801
• 关键词: Address; Algorithms; Biomedical Research; Callback; Chemicals; Code; Communities; Computer software; Custom; Development; Disease; Evaluation; Free Energy; Goals; Ligand Binding; Medical Research; Methodology; Methods; Modernization; Modification; Molecular; Performance; Physiological; Research; Resources; Sampling; Scientist; Software Engineering; Statistical Mechanics; System; Technology; Testing; Thermodynamics; Validation; Work; base; computing resources; flexibility; human disease; improved; innovation; insight; interest; interoperability; molecular dynamics; open source; parallel computer; parallelization; public health relevance; simulation; simulation software; tool

 DESCRIPTION (provided by applicant): Advances in molecular simulation methods and hardware have finally made possible the simulation of biomolecules on physiological timescales. Such simulations provide an important tool to aid the molecular understanding of disease. However, fully integrating these new tools into medical research requires that simulation software becomes easier to use, easier to develop for, and more hardened, reliable and robust. Making these capabilities accessible and reliable in the hands of a broad scientific community will require transformative gains in reliability, interoperability, flexibility, and ease of use atscale. We therefore propose improvements to the open-source Gromacs molecular simulation package to help meet these challenges. These improvements will 1) enable automated tests of physical validity for both code contributions and simulation parameter choices, 2) provide a simple interface for external code to utilize Gromacs functionality, and 3) provide a high-performance interface to mix Monte Carlo and molecular dynamics simulation. This work will facilitate community extension via a robust testing framework integrated with our code review system and via an API to allow implementation of new tools and simulations using high-level calls. These efforts will leverage best practices from software engineering and be implemented in a way to put tools in the hands of a broad developer and user community.