Grafton Anthony K
Division of Science, Lyon College, P.O. Box 2317, Batesville, Arkansas 72503, USA.
J Comput Chem. 2007 May;28(7):1290-305. doi: 10.1002/jcc.20642.
This report describes the development and applications of a software package called Vibalizer, the first and only method that provides free, fast, interactive, and quantitative comparison and analysis of calculated vibrational modes. Using simple forms and menus in a web-based interface, Vibalizer permits the comparison of vibrational modes from different, but similar molecules and also performs rapid calculation and comparison of isotopically substituted molecules' normal modes. Comparing and matching complex vibrational modes can be completed in seconds with Vibalizer, whereas matching vibrational modes manually can take hours and gives only qualitative comparisons subject to human error and differing individual judgments. In addition to these core features, Vibalizer also provides several other useful features, including the ability to automatically determine first-approximation mode descriptions, to help users analyze the results of vibrational frequency calculations. Because the software can be dimensioned to handle almost arbitrarily large systems, Vibalizer may be of particular use when analyzing the vibrational modes of complex systems such as proteins and extended materials systems. Additionally, the ease of use of the Vibalizer interface and the straightforward interpretation of results may find favor with educators who incorporate molecular modeling into their classrooms. The Vibalizer interface is available for free use at http://www.compchem.org, and it is also available as a locally-installable package that will run on a Linux-based web server.
本报告介绍了一个名为Vibalizer的软件包的开发与应用，它是首个也是唯一一种能够提供免费、快速、交互式且定量的计算振动模式比较与分析的方法。通过基于网页界面中的简单表单和菜单，Vibalizer允许对来自不同但相似分子的振动模式进行比较，还能对同位素取代分子的简正模式进行快速计算和比较。使用Vibalizer，几秒内就能完成复杂振动模式的比较和匹配，而手动匹配振动模式可能需要数小时，且只能给出定性比较，还容易出现人为误差和不同的个人判断。除了这些核心功能外，Vibalizer还提供了其他一些有用的功能，包括自动确定一阶近似模式描述的能力，以帮助用户分析振动频率计算结果。由于该软件可设置为处理几乎任意大小的系统，在分析蛋白质和扩展材料系统等复杂系统的振动模式时，Vibalizer可能会特别有用。此外，Vibalizer界面的易用性和结果的直观解读可能会受到将分子建模纳入课堂教学的教育工作者的青睐。Vibalizer界面可在http://www.compchem.org免费使用，它也可以作为一个可在基于Linux的网络服务器上运行的本地可安装包获取。
