All-atom automatic OPLS-AA topology generator

Published in �� 30th, 2015

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 […]

Scanning PES ab initio and in MM

Published in �� 19th, 2015

Posted by comcon1 in ��

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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.

Lipid membrane MD modeling with GROMACS

Published in �� 20th, 2014

Posted by comcon1 in ��

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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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Published in �� 16th, 2014

Posted by comcon1 in ��

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Python membrane generator for MD simulations

Published in �� 29th, 2011

Posted by comcon1 in ��

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Download script: memgen-0.0.1.tar.gz System requirements: python 2 (2.6 and higher), python openbabel library, python numpy library. 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 lipid compounds (e.g. cholesterol). Molecules are positioned according to hexagonal packing grid. […]

Normal modes visualization for PyMol

Published in �� 16th, 2011

Posted by Peter Mamonov in ��

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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 […]

Nanotubes generating script for PyMol

Published in �� 16th, 2011

Posted by Peter Mamonov in ��

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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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