Collaborative Research: Development and Application of the AMOEBA Polarizable Force Field

合作研究：AMOEBA极化力场的开发与应用

• 批准号: 1152823
• 负责人: Jay Ponder
• 金额: $ 25.8万
• 依托单位: Washington University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1152823&HistoricalAwards=false
• 关键词: Collaborative; Research; Development; Application; AMOEBA

Jay Ponder of Washington University in Saint Louis and David Gohara of Saint Louis University are supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry, and the Office of Cyberinfrastructure to improve the accuracy of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field model for molecular simulation and to increase the range of applicability of the model via parallelization of the underlying TINKER molecular modeling software. In this project, the researchers develop new terms for an AMOEBA-2 model that encompass physical effects missing from the original AMOEBA force field. In particular, charge transfer, penetration effects and damped short-range dispersion terms are being parameterized to remove the largest remaining systematic inaccuracies. Comparison of the resulting short-range energetic model against quantum mechanical calculations allow correct partitioning of internal energy into the various terms, and provide a consistent basis for improving AMOEBA-2. The existing TINKER code as well as the new energy terms are being parallelized using a hybrid OpenMP and MPI paradigm. The resulting new potential and software will be applied to two current problems that require both extensive simulation and a high level of accuracy: prediction of organic crystal structures, and computation of ligand binding in host-guest complexes. Both of these problem areas have long represented "holy grail" applications for the field of computational chemistry.Molecular force field calculations are important tools in computational biophysics, structure determination of bio-macromolecules, molecular design, and modeling of the properties of molecules and materials. Methods, algorithms and software developed under this project are being made available to the broader community via periodic release of new versions of the TINKER molecular modeling package. This package is widely used in academic research labs and in the chemical and pharmaceutical industries worldwide. The team is also involved in educational activities through University courses, as well as the provision of tutorial materials and laboratory exercises for instructors wishing to use the TINKER software in their own teaching.

圣路易斯华盛顿大学的 Jay Ponder 和圣路易斯大学的 David Gohara 获得了化学系化学理论、模型和计算方法项目以及网络基础设施办公室的资助，以提高用于分子模拟的 AMOEBA（生物分子应用原子多极优化能量学）力场模型的准确性，并通过并行化来提高模型的适用范围。 底层 TINKER 分子建模软件。 在这个项目中，研究人员为 AMOEBA-2 模型开发了新术语，其中包含原始 AMOEBA 力场中缺失的物理效应。特别是，电荷转移、穿透效应和阻尼短程色散项正在被参数化，以消除最大的剩余系统误差。将所得的短程能量模型与量子力学计算进行比较，可以将内部能量正确划分为各个项，并为改进 AMOEBA-2 提供一致的基础。现有的 TINKER 代码以及新能源术语正在使用混合 OpenMP 和 MPI 范例进行并行化。由此产生的新潜力和软件将应用于当前需要广泛模拟和高精度的两个问题：有机晶体结构的预测和主客体复合物中配体结合的计算。这两个问题领域长期以来一直代表着计算化学领域的“圣杯”应用。分子力场计算是计算生物物理学、生物大分子结构测定、分子设计以及分子和材料特性建模的重要工具。通过定期发布新版本的 TINKER 分子建模包，该项目开发的方法、算法和软件可供更广泛的社区使用。该软件包广泛应用于学术研究实验室以及全球化学和制药行业。该团队还通过大学课程参与教育活动，并为希望在自己的教学中使用 TINKER 软件的教师提供教程材料和实验室练习。