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molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2018-02-21 , DOI: 10.1002/jcc.25189
Henrique S. Fernandes 1 , Maria J. Ramos 1 , Nuno M. F. S. A. Cerqueira 1
Affiliation  

The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations. The starting structures for these calculations can be imported from different chemical formats. A set of tools is available to help the user to examine or modify any geometry parameter. This includes the definition of layers in ONIOM calculations, choosing fixed atoms during geometry optimizations, the recalculation or adjustment of the atomic charges, performing SCANs or IRC calculations, etc. molUP also extracts the geometries from the output files as well as the energies of each of them. All of these tasks are performed in an interactive GUI that is extremely helpful for the user. MolUP was developed to be easy to handle by inexperienced users, but simultaneously to be a fast and flexible graphical interface to allow the advanced users to take full advantage of this plugin. The program is available, free of charges, for macOS, Linux, and Windows at the PortoBioComp page https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup. © 2018 Wiley Periodicals, Inc.

中文翻译:

molUP:使用高斯软件处理 QM 和 ONIOM 计算的 VMD 插件

计算(生物)化学取得的显着进步使其在许多科学领域得到广泛应用,特别是在反应机制研究中。这些研究涉及大量复杂的计算,这些计算通常使用高斯程序套件进行。输入文件的准备和输出文件的分析并非易事,而且往往涉及费力和复杂的步骤。考虑到这一点,我们开发了 molUP:一个 VMD 插件,它提供了一整套工具,可增强 QM 和 ONIOM(QM/MM、QM/QM 和 QM/QM/MM)计算的准备。这些计算的起始结构可以从不同的化学格式导入。一组工具可帮助用户检查或修改任何几何参数。这包括 ONIOM 计算中层的定义,在几何优化、重新计算或调整原子电荷、执行扫描或 IRC 计算等过程中选择固定原子。 molUP 还从输出文件中提取几何形状以及每个文件的能量。所有这些任务都是在对用户非常有帮助的交互式 GUI 中执行的。MolUP 的开发是为了让没有经验的用户易于操作,但同时也是一个快速灵活的图形界面,允许高级用户充分利用这个插件。该程序可在 PortoBioComp 页面 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup 上免费获得,适用于 macOS、Linux 和 Windows。© 2018 Wiley Periodicals, Inc. 执行扫描或 IRC 计算等。 molUP 还从输出文件中提取几何形状以及每个文件的能量。所有这些任务都是在对用户非常有帮助的交互式 GUI 中执行的。MolUP 的开发是为了让没有经验的用户易于操作,但同时也是一个快速灵活的图形界面,允许高级用户充分利用这个插件。该程序可在 PortoBioComp 页面 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup 上免费获得,适用于 macOS、Linux 和 Windows。© 2018 Wiley Periodicals, Inc. 执行扫描或 IRC 计算等。 molUP 还从输出文件中提取几何形状以及每个文件的能量。所有这些任务都是在对用户非常有帮助的交互式 GUI 中执行的。MolUP 的开发是为了让没有经验的用户易于操作,但同时也是一个快速灵活的图形界面,允许高级用户充分利用这个插件。该程序可在 PortoBioComp 页面 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup 上免费获得,适用于 macOS、Linux 和 Windows。© 2018 Wiley Periodicals, Inc. MolUP 的开发是为了让没有经验的用户易于操作,但同时也是一个快速灵活的图形界面,允许高级用户充分利用这个插件。该程序可在 PortoBioComp 页面 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup 上免费获得,适用于 macOS、Linux 和 Windows。© 2018 Wiley Periodicals, Inc. MolUP 的开发是为了让没有经验的用户易于操作,但同时也是一个快速灵活的图形界面,允许高级用户充分利用这个插件。该程序可在 PortoBioComp 页面 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup 上免费获得,适用于 macOS、Linux 和 Windows。© 2018 Wiley Periodicals, Inc.
更新日期:2018-02-21
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