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

这项探索性研究小额拨款申请提出了一系列初步研究，用于开发隐式溶剂模型（ISM），用于分子动力学和大型分子系统的蒙特卡罗模拟。提出的ISM的目标是将大量溶剂效应的描述和大分子微环境的计算纳入描述系统的经验势函数中。随着计算能力的提高和许多不同模拟算法的可用性，对现实尺寸的生物系统进行模拟成为可能。然而，这些模拟必须在实际计算时间内对溶剂环境进行令人满意的考虑。提出的ISM应该通过消除在模拟系统中包含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.