OPLS-AA patch for different types of molecules

Published in �� 8th, 2016

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.

Reaction-diffusion systems in 2D space with python

Published in �� 26th, 2016

Posted by comcon1 in ��

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In our previous article (<a href=»http://erg.biophys.msu.ru/wordpress/archives/706» alt=»discrete Laplacian»>about construction of the discrete Laplacian with numpy</a>) 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 […]

Scanning PES ab initio and in MM

Published in �� 19th, 2015

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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.

Quantum chemistry information page

Published in �� 19th, 2015

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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.

Python script for processing FRAP image set

Published in �� 19th, 2015

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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 […]

Using Firefly/GAMESS-US efficiently

Published in �� 30th, 2015

Posted by comcon1 in ��

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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.

Building and plotting Fukui function with FireFly and PyMol

Published in �� 28th, 2014

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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).

Lipid membrane MD modeling with GROMACS

Published in �� 20th, 2014

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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 […]

Using spherical functions (from A.Granovsky manual)

Published in �� 9th, 2014

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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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Published in �� 16th, 2014

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