Advanced Electrostatic Computation in Molecular Dynamics

分子动力学中的高级静电计算

基本信息

批准号：
6882566
负责人：
ALEXANDER H BOSCHITSCH
金额：
$ 9.98万
依托单位：
CONTINUUM DYNAMICS, INC.
依托单位国家：
美国
项目类别：
财政年份：
2005
资助国家：
美国
起止时间：
2005-05-01 至 2006-10-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/6882566
关键词：
Advanced Electrostatic Computation Molecular Dynamics

项目摘要

DESCRIPTION (provided by applicant): Advances in computational hardware and molecular modeling techniques have revolutionized our ability to simulate electrostatic interactions which play a fundamental role in the stability, structure, folding and function of bio-molecules. Currently, the continuum electrostatic description based upon the Poisson- Boltzmann Equation (PBE) offers the best combination of modeling fidelity and computational cost. While very large bio-molecular assemblies such as ribosomes, containing hundreds of thousands of atoms, have been successfully solved using PBE solvers, major difficulties are encountered when these solvers are incorporated into molecular dynamics (MD) and energy minimization (EM) codes. Impaired accuracy of predicted electrostatic field at molecular surfaces destabilizes MD simulations and hinders convergence in EM computations. The proposed effort will provide new computational tools to accurately and efficiently predict the required electrostatic properties near the molecular surface. Previous technology, notably a novel adaptive Cartesian grid structure that maximizes computational performance for large-scale bio-molecules, will be modified to achieve high accuracy at the surface. The resulting computational tool should prove invaluable to: (i) MD and EM calculations by efficiently providing high fidelity, PBE-quality electrostatic energy gradients and (ii) researchers interested in relating electrostatic surface properties (e.g., potential and induced charge) to bio-molecular function.

描述（由申请人提供）：计算硬件和分子建模技术的进展彻底改变了我们模拟静电相互作用的能力，这些静电相互作用在生物分子的稳定性，结构，折叠和功能中起着基本作用。目前，基于Poisson-Boltzmann方程（PBE）的连续静电描述提供了建模保真度和计算成本的最佳组合。尽管使用PBE求解器成功求解了非常大的生物分子组件，例如核糖体（核糖体），当这些求解器纳入分子动力学（MD）和能量最小化（EM）代码时，遇到了重大困难。在分子表面预测的静电场的准确性受损，使MD模拟不稳定，并阻碍EM计算中的收敛性。提出的工作将提供新的计算工具，以准确有效地预测分子表面附近所需的静电性能。以前的技术，尤其是一种新型的自适应笛卡尔网格结构，可最大程度地提高大规模生物分子的计算性能，以在表面上实现高精度。最终的计算工具应有效地证明：（i）MD和EM计算通过有效提供高富度，PBE质量静电能梯度以及（II）有兴趣将静电表面特性（例如电位和诱导电荷）与生物分子功能相关的研究人员。