FRAP kinetics can be measured from image series directly with numpy libraries. However sometimes it is necessary to remove motion of the sample before measuring fluorescence intensity. In such a case it is possible to use normalized cross-correlation technique. Here we provide script that helps you to remove sample motion and obtain FRAP kinetics from […]

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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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(ATTENTION! MATERIAL UPDATED!) For lipid bilayer modelling the whole toolchain was built: from creating membranes to MD trajectory analysis. We use OPLS-AA forcefield with Berger potentials for alcane dihedrals integrated. Addings to OPLS-AA Forcefield. We use OPLS-AA with some includings; «includings» are overlays on the standart GROMACS forcefield files. Patch for GROMACS OPLS-AA forcefield  is […]

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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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Задача направлена на знакомство с азами методов молекулярного моделирования. Основной ее целью является знакомство студентов с методом молекулярной динамики на примере пакета программ GROMACS и освоение ими базовых операций, необходимых для успешной постановки молекулярно-динамических расчетов, а также обработки и визуализации полученных данных. Объектом исследования в рамках задачи был выбран случайный полипептид, состоящий из 7-ми аминокислотных […]

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The following application solves 1d Schrodinger equation in user defined potential. The app is written in Python and uses Numpy,SciPy for linear algebra and Matplotlib for visualization. The program can be used as a standalone application as well as python module implementing relevant calculations. Atomic units are used througout the interface. The precision of calculations […]

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This PyMol script is capable of generating a set of a molecule’s conformations, which can be further used to calculate their potential energy or any other properties. The script enables one to vary several internal degrees of freedom (DOFs) synchronously as well as scanning over a multidimensional grid in a space of DOFs. To use […]

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Построение лицеприятных графиков в matplotlib сопряжено с рядом технических трудностей. Для того, чтобы график был хорошо читаем приходится настраивать большое количество параметров, как то шрифт подписей, толщину линий ошибки, легенду, частоту подписей осей, шаг сетки и многое другое. В данной статье подробно разбирается построение одного графика, на примере которого Вы можете составить свой собственный скрипт.

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