This task is devoted to introduce GROMACS notation for force fields. We build the model of hydrazine molecule, introducing lone electron pair as an artificial atom. We set molecular conformations with pairs or by defining dihedral potential. Varying dihedral potentials or pairs we obtain different equilibrium conformations of hydrazine.

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В данном материале публикуется указатель на видеозаписи первой версии теоретической части курса «Теория и практика молекулярно-динамических расчетов», прочитанного А. Нестеренко и Д. Зленко для магистрантов 2го года кафедры биофизики биологического факультета МГУ. В курсе излагаются теоретические основы проведения и обработки молекулярно-динамических расчетов. Материал достаточно сложный и не рекомендуется тем, кто хочет ознакомиться с тем, что […]

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ERG group members work with different types of molecules and consequently added new atomtypes into classical OPLS-AA distributed with GROMACS. Now the ERG patch of OPLS-AA force field is published at bitbucket as a repository.

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In our previous article about construction of the discrete Laplacian with numpy we discuss the discrete Laplacian calculation for numerical solving of diffusion PDE. Here we generalize this technique for the  two-dimensional space. We describe the complete algorithm of solving of reaction-diffusion equations with implementation of Crank-Nicolson scheme for diffusion part together with Runge-Kutta scheme for […]

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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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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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(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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