WEB BASED DOCUMENTATION & TUTORIALS FOR YAMMP

充足的在线文档对任何广泛的 使用分子建模软件包。由于YAMMP最初是开发的 仅供阿拉巴马大学伯明翰分校(UAB)使用， 以前，文件并不被视为一个关键问题。 随着这一研究资源的建立和一系列新的 与UAB以外的科学家合作，适当的文档 成为一个高度优先的问题。我们决定利用网络的优势 技术，我们已经开始开发完整的在线 YAMMP的文档。从一开始，我们就将 培训新用户的一系列在线教程的文档 在使用YAMMP建模的原则和实践中 大分子系统。该教程包包含针对以下目标的模块 经验丰富的模型师和结构生物学家：他们专注于 低分辨率YAMMP模式中的经验力场。另一个 一组模块针对的是新手建模者： 烷烃教授分子力学的基本原理， 包括力场和算法(能量最小化；分子 动力学；蒙特卡罗；模拟退火法)。因为这些教程 假设有某些基本的数学技能，我们也在发展 帮助学生根据需要更新或学习这些技能的教程： 这些概念包括正态分布、波尔兹曼 分布、傅里叶分析等。

Adequate on-line documentation is a great asset for any widely used molecular modeling package. Since YAMMP was originally developed only for use at the University of Alabama at Birmingham (UAB), documentation had not previously been regarded as a critical issue. With the establishment of this Research Resource and a series of new collaborations with scientists outside UAB, proper documentation became a high priority. We decided to take advantage of web technology, and we have begun developing complete on-line documentation for YAMMP. From the beginning, we have coupled the documentation to a series of on-line tutorials for educating new users in the principles and practices of using YAMMP for modeling macromolecular systems. The tutorial package has modules aimed at experienced modelers and structural biologists: these focus on the empirical force field used in low resolution YAMMP models. Another set of modules is aimed at the novice modeler: these use simple alkanes to teach the basic principles of molecular mechanics, including force fields and algorithms (energy minimization; molecular dynamics; Monte Carlo; simulated annealing). Since the tutorials assume certain basic mathematical skills, we are also developing tutorials to help students refresh or learn those skills as necessary: these include such concepts as the normal distribution, the Boltzmann distribution, Fourier analysis, and so on.