Малый практикум по квантовой химии проводится для студентов-биофизиков 3го курса и других желающих. Ведущие: Алексей Нестеренко и Дмитрий Зленко. Место проведения: компьютерный класс корпуса ЛИК (Ленинские горы 1, корп. 12). Даты: 26-30 июня 2017 года Практикум призван обучить азам квантовой химии с нуля. Примерная программа: Работа в командной строке linux Работа в PyMOL: визуализация и редактирование молекулярных структур […]

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Here is the tutorial about how to scan potential energy over specific internal coordinate (e.g. dihedral angle) ab initio and then transfer this trajectory into molecular mechanics package and compare them.

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On this page we collect references to our resources, documentation and resources on other sites. All these data are very helpful for everybody who wants to learn practical quantum chemistry.

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Here we introduce several hooks that improove calculation speed. 1) Using GUESS=MOREAD and other «continuators» to fast continue broken calculation. 2) Using delocalized coordinates and Z-matrix to improove geometry optimization convergency. 3) Preoptimization with pure basis set and theory level.

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Fukui functions shows the level of reactivity of different places in a complex molecule. They can be easily plotted with GabEdit software but it has a pure functions of chemical drawing. PyMol is a powerful drawing instrument and here we show how to plot Fukui function with PyMOL after two calculation steps with FireFly (PC-GAMESS).

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With QM software like GAMESS/Firefly it is possible to obtain much information about a molecule in text format. There exist some «envelope» software like Gabedit or WxMacMolPlt that could help you to visualize this information. Here we provide some instructions that will allow you to make your own visualization using powerful abilities of PyMol. Below […]

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The manual to FireFly program clearly explain why and how to use spherical or cartesian functions when working with different basis sets. Here we publish this part of manual. The fresh and whole manual you can find at the FireFly website, it is free for download and is very useful for both Firefly users and […]

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To build topology for the new molecule partial charges for atoms should be determined. Working in OPLS force field big amount of atom types with predefined partial charges allows you to chose atom type for almost every atom of your «new» compound. But In rest force fields you have no choice except use quantum chemistry […]

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