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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OPLS-AA topology generation is a very complex task because of huge amount of the atomtypes described this force field. The OPLS-AA force filed contains more than 800 atom types that is nevertheless not sufficient for describing all the diversity of chemical structures. Thus, as parameters for new chemical fragments appears in literature the atomtype database […]

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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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(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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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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Download script: memgen-0.0.2.tar.gz System requirements: python 2 (2.6 and higher), python openbabel library, python numpy library. Updates in new version (2016 sep): supports multi-residual lipids, numerates lipids correctly. If you are looking for topologies and structure files for lipids please read this post. The memgen script makes a bilayer membrane from different phospholipids and other […]

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This script allows one to visualize normal modes, calculated with GROMACS package, using PyMol. In particular the script loads Hessian matrix from an .mtx file produced by Gromacs, solves for it’s eigenvectors and eigenvalues and prints them out, and finally produce several frames corresponding to selected vibrational mode. See related media in the end of […]

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The script generates nanotubes of arbitrary structure. See related media in the end of the page. To use it, save script to some file, then load into PyMol with the command: PyMol> run /path/to/script.py then issue the command: PyMol> ntgen obj_name, n, m, l This will produce an object «obj_name», containing SWNT characterized by two […]

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