Postdoc: Novel Computational Approaches to Free Energy Perturbation Calculations

这一建议的目的是发展新的和有效的计算方法来计算自由能摄动（FEP）。FEP计算在高性能并行计算系统上广泛应用，在帮助解开生物大分子的结构、动力学和热力学问题方面具有巨大的潜力。在这个项目中，他们将(a)探索化学FEP计算的新扩展系统方法的发展，这种方法允许与化学坐标中的“进展”相关的传统变量动态演变；(b)系统地确定采样中使用的保护伞或偏置电位；(c)开发新技术，进一步扩展和自动化处理方法，提高加权直方图分析方法的误差分析能力。

Brooks 9503998 The objective of this proposal is the development novel and efficient computational approaches to free energy perturbation (FEP) calculations. FEP calculations, carried out extensively on high performance parallel computing systems, hold a great potential for assisting the unraveling of questions regarding structure, dynamics and thermodynamics of biological macromolecules. In this project they will (a) explore the development of new extended sytem methods for chemical FEP calculations which allow the conventional variables associated with "progress" in the chemical coordinates to evolve dynamically; (b) systematically determine an umbrella or biasing potential used in sampling, (c) develop new techiques to further extend and automate the processing methods and advance the error analysis capabilities of weighted histogram analysis method.