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: 9103494
• 负责人: Peter M Kasson
• 金额: $ 28.49万
• 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/9103494
• 关键词: Address; Algorithms; Biomedical Research; Callback; Chemicals; Code; Communities; Computer software; Computing Methodologies; Custom; Development; Disease; Evaluation; Free Energy; Goals; Ligand Binding; Medical Research; Methods; 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; meetings; molecular dynamics; open source; parallel computer; parallelization; programs; 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.

 描述（由申请人提供）：分子模拟方法和硬件的进步最终使得在生理时间尺度上模拟生物分子成为可能。这样的模拟提供了一个重要的工具，以帮助分子理解疾病。然而，将这些新工具完全集成到医学研究中需要仿真软件变得更容易使用，更容易开发，并且更加坚固，可靠和强大。要使这些能力在广泛的科学界手中变得可用和可靠，就需要在可靠性、互操作性、灵活性和大规模易用性方面取得变革性进展。因此，我们建议改进开源Gromacs分子模拟包，以帮助应对这些挑战。这些改进将1）实现对代码贡献和模拟参数选择的物理有效性的自动化测试，2）为外部代码提供简单的接口以利用Gromacs功能，以及3）提供高性能接口以混合Monte Carlo和分子动力学模拟。这项工作将通过与我们的代码审查系统集成的强大测试框架和API来促进社区扩展，以允许使用高级调用实现新工具和模拟。这些努力将利用软件工程的最佳做法，并以一种将工具交到广大开发人员和用户社区手中的方式加以实施。