Hardening and Development of the GROMACS Molecular Simulation Engine

GROMACS 分子模拟引擎的强化和开发

基本信息

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
项目类别：
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

项目摘要

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，这种模拟提供了帮助分子理解疾病的重要工具。然而，将这些新工具完全整合到医学研究中。要求仿真软件变得更易于使用、更易于开发，并且更加坚固、可靠和强大，要使这些功能能够在广泛的科学界中使用和可靠，将需要在可靠性、互操作性、灵活性和易用性方面取得变革性的进步。使用因此，我们建议对开源 Gromacs 分子模拟包进行改进，以帮助应对这些挑战，这些改进将 1) 实现代码贡献和模拟参数选择的物理有效性的自动测试，2) 为外部代码提供简单的接口。利用 Gromacs 功能，3) 提供高性能接口来混合蒙特卡罗和分子动力学模拟。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以及允许实施新工具的 API 来促进社区扩展。和使用高级调用的模拟。这些将利用软件工程工作的最佳实践，并以将工具交到广泛的开发人员和用户社区手中的方式实施。