Grid convergence of PyGBe with protein G B1 D4

This file bundle contains data, running script and final plot of grid-convergence study for protein G B1 D4' near a charged surface. The running script invokes the bioelectrostatics solver (PyGBe) with the given input data, computes the extrapolated value of solvation plus surface energy (with Richardson extrapolation), and plots the final result of convergence. This result is part of an upcoming paper. Publication information will be updated at the time of submission with the arXiv pre-print number, and at the time of publication with the final citation. PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: <em>—"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods,"</em> Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers," Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>,<strong> 185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.

本文件包包含针对带电表面附近的G蛋白B1结构域D4'所开展的网格收敛性研究（grid-convergence study）的相关数据、运行脚本与最终绘图结果。本运行脚本将调用生物静电求解器PyGBe，结合给定输入数据，采用理查森外推法（Richardson extrapolation）计算溶剂化能与表面能之和的外推值，并绘制收敛性最终结果。该研究成果属于一篇待发表论文的内容。投稿时将更新预印本的arXiv编号，正式发表后将更新完整引用信息。

PyGBe采用隐式溶剂模型（泊松-玻尔兹曼模型，Poisson-Boltzmann）求解生物分子静电学问题，并依托GPU硬件实现高速计算。该代码基于Python、PyCUDA与CUDA编写。有关PyGBe代码的更多信息可参考以下文献：
—"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods"，Christopher Cooper、Lorena A. Barba，figshare平台，DOI：10.6084/m9.figshare.154331。
—"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers"，Christopher D. Cooper、Jaydeep P. Bardhan、L. A. Barba，*Comput. Phys. Comm.*，第185卷第3期，第720至729页（2014年3月），DOI：10.1016/j.cpc.2013.10.028，预印本arXiv:1309.4018。

致谢：
本研究获美国海军研究办公室（Office of Naval Research）应用计算分析项目（项目编号：N00014-11-1-0356）资助。LAB同时感谢美国国家科学基金会CAREER奖（项目编号：OCI-1149784）的支持。