SGER: An Implicit Solvent Model for Fast Computer Simulations on Biological Systems

这项为探索性研究提供小额赠款的请求提出了一系列初步研究，以开发用于大分子体系的分子动力学和蒙特卡罗模拟的隐式溶剂模型(ISM)。提出的ISM的目标是将对本体溶剂效应的描述和对大分子微环境的考虑纳入到描述体系的经验势函数中。随着计算能力的提高和许多不同的模拟算法的出现，尝试在真实规模的生物系统上进行模拟成为可能。然而，这些模拟必须包括在实际计算时间内令人满意地考虑溶剂环境。建议的ISM应该通过消除在模拟体系中包括大量显式溶剂分子的需要来实现这一目标。

This request for a Small Grant for Exploratory Research proposes an initial series of studies for the development of an implicit solvent model (ISM) for use with molecular dynamics and Monte Carlo simulations on large molecular systems. The objective of the proposed ISM is to incorporate the description of bulk solvent effects and an accounting of the macromolecule's microenvironment into the empirical potential function describing the system. With the increase in compute-power and the availability of many different simulation algorithms, it becomes possible to attempt simulations on biological systems of the realistic size. However, these simulations must include satisfactory consideration of the solvent environment in practicable computing times. The proposed ISM should achieve this goal by eliminating the need to include a large number of explicit solvent molecules in the simulated system.