SI2-CHE: Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces

SI2-CHE：先进势能面化学软件的开发和部署

• 批准号: EP/K040138/1
• 负责人: Lorna Smith
• 金额: $ 46.04万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FK040138%2F1
• 关键词: SI2; CHE; Development; Deployment; Chemical

Molecular dynamics simulations provide a powerful tool to study a wide range of chemical and biochemical systems. The simulations provide a movie of the atoms diffusing over time, from which important dynamic and thermodynamic properties may be calculated. The reliability of these simulations is, however, limited by the accuracy of the model used to describe how the atoms in the system interact with each other. Conventional force fields, in which fixed charges are used, represent a major factor limiting the successful application of computer simulations to a variety of grand challenge problems in computational chemistry, biochemistry and materials science. Polarizable empirical force fields, which offer a clear and systematic improvement by allowing atom-centred charges to change depending on their environment, have been recently developed by most major research groups in force field development to increase accuracy. These advanced potential energy surfaces are important for the future of grand challenge applications such as the design of environmentally friendly materials, chemical reactions and reactivity critical for chemical synthesis, and biological complexity such as protein-drug interactions.However, there are obstacles to using advanced potential energy surfaces for these grand challenge chemistry problems: the computational cost of the models, limited dissemination to a broad range of community codes, and lagging quality software implementations on HPC architectures and newer GPU and multicore hardware. To address these issues, we have organized a UK and US consortium that represents a broad cross section of the computational chemistry software community involved in chemical and biochemical applications, force field development, electronic structure methods, molecular dynamics algorithms, and software engineering with computer science experts. In this project, state-of-the-art polarizable potential energy functions will be consistently implemented and tested in a number of the most widely used simulation codes. The latest software development practices will be used to ensure that the freely-available developed software meets the highest standards of robustness, maintainability, and usability. New methodologies to improve the computational performance of these models will also be implemented. An important aspect of our work is to combine these latest force field models with quantum mechanical methods, allowing the accurate modelling of chemical reactivity and excited states. Our international collaboration between US and UK universities and HPC centres will ensure that the investment made in molecular simulation software is successfully deployed on current and emergent hardware and will also realize a long term payoff in community availability and sustainability. This project will lead to a step-change in the use of advanced potential energy surfaces by delivering consistent and sustainable implementations of the latest science on a diverse range of readily available and widely utilised software platforms.

分子动力学模拟为研究广泛的化学和生物化学系统提供了强有力的工具。模拟提供了原子随时间扩散的电影，从中可以计算出重要的动力学和热力学性质。然而，这些模拟的可靠性受到用于描述系统中原子如何相互作用的模型的准确性的限制。传统的力场，其中使用固定电荷，代表了一个主要因素，限制了成功应用计算机模拟的各种重大挑战问题，在计算化学，生物化学和材料科学。可极化的经验力场，它提供了一个明确的和系统的改进，允许原子为中心的电荷改变取决于他们的环境，最近已开发的力场发展，以提高精度的大多数主要研究小组。这些先进的势能面对于未来的重大挑战应用非常重要，例如环境友好材料的设计，化学合成的关键化学反应和反应性，以及生物复杂性，例如蛋白质-药物相互作用。然而，将先进的势能面用于这些重大挑战化学问题存在障碍：模型的计算成本、对广泛的社区代码的传播有限，以及HPC架构和更新的GPU和多核硬件上的软件实现质量落后。为了解决这些问题，我们组织了一个英国和美国的财团，代表了广泛的横截面的计算化学软件社区参与化学和生物化学应用，力场开发，电子结构方法，分子动力学算法，和软件工程与计算机科学专家。在这个项目中，国家的最先进的极化势能函数将始终实施和测试中最广泛使用的模拟代码。将采用最新的软件开发做法，以确保免费开发的软件符合稳健性、可维护性和可用性的最高标准。还将采用新的方法来提高这些模型的计算性能。我们工作的一个重要方面是将这些最新的力场模型与量子力学方法结合联合收割机，从而精确地模拟化学反应性和激发态。我们与美国和英国大学以及HPC中心之间的国际合作将确保在分子模拟软件方面的投资成功部署在当前和新兴的硬件上，并将在社区可用性和可持续性方面实现长期回报。该项目将通过在各种现成和广泛使用的软件平台上提供最新科学的一致和可持续的实施，导致先进势能表面使用的逐步变化。

项目成果

Producing robust, sustainable and high performance software for complex potential energy models

为复杂的势能模型生产强大、可持续和高性能的软件

• 发表时间: 2016
• 作者: Filinger W