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.

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 Cyber​​infrastructure 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基础修补匠分子建模软件。 在这个项目中，研究人员为Amoeba-2模型开发了新的术语，该模型涵盖了原始变形虫力场中缺少的物理效果。特别是，电荷转移，渗透效应和阻尼的短距离色散项正在参数中，以消除剩余的系统不准确性。将所得的短距离能量模型与量子机械计算的比较允许将内部能量正确分配到各种术语中，并为改善AmoeBA-2提供了一致的基础。现有的修补剂代码以及新的能量术语正在使用Hybrid OpenMP和MPI范式并行。由此产生的新电位和软件将应用于需要大量仿真和高度准确性的两个当前问题：预测有机晶体结构，以及在宿主 - 阵线复合物中配体结合的计算。这两个问题领域长期以来都代表了计算化学领域的“圣杯”应用。分子力场计算是计算生物物理学的重要工具，生物大分子的结构确定，分子设计以及分子和材料的性质的建模。通过定期发布Tinker Molecular Modeling Package的新版本，可以在此项目下开发的方法，算法和软件。该软件包广泛用于全球学术研究实验室以及化学和制药行业。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。