In this article we considerљcalculationљof discrete Laplacian for 1D arrays usingљpython/numpy/scipy. We introduceљthe sparse matrix technique that is rather efficient for computation of certain types of diffusion PDE.
Constructing discrete Laplacian via sparse matrix
Published in Январь 24th, 2016
Posted by admin in Без рубрики
1 Comment
Scanning PES ab initio and in MM
Published in Май 19th, 2015
Posted by comcon1 in Без рубрики
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.
Python script for processing FRAP image set
Published in Май 19th, 2015
Posted by comcon1 in Без рубрики
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 […]
Visualize partial charges in PyMol
Published in Октябрь 30th, 2014
Posted by admin in Без рубрики
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 […]
1D Schrodinger equation in arbitrary potential
Published in Апрель 25th, 2014
Posted by Peter Mamonov in Без рубрики
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 […]
PyMol script for scanning potential energy surfaces
Published in Декабрь 9th, 2013
Posted by Peter Mamonov in Без рубрики
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 […]
Пример построения графика в matplotlib
Published in Октябрь 7th, 2013
Posted by comcon1 in Без рубрики
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.
Подбор оптимального растяжения сегмента сосуда («нормализация»)
Published in Июнь 16th, 2013
Posted by Peter Mamonov in Без рубрики
Скачать программу (правая кнопка — сохранить как) Дополнительное ПО, необходимое для корректной работы программы под Windows
Инструкции по установке программы TRAX
Published in Февраль 12th, 2013
Posted by Peter Mamonov in Без рубрики
Программа TRAX позволяет численно решать системы обыкновенных дифференциальных уравнений и визуализировать решение в виде графиков от времени либо траекторий на фазовой плоскости. Также программа позволяет численно решать системы разностных (дискретных) уравнений. Для уcтановки программы необходимо выполнить следующие действия: Установить интерпретатор языка Python и набор вспомогательных библиотек, входящих в состав Enthought Python Distribution (EPD). Скачать EPD […]
Phase plane explorer
Published in Март 29th, 2012
Posted by Peter Mamonov in Без рубрики
This small program named TRAX is capable of solving systems of ordinary differential equations and plotting the solution on a phase plane as well as function of time. The program is intended for educational purposes. See picture below for interface and capabilities overview as well as usage reference. The program runs on any Python-enabled platform, […]
Метки
Последние записи
- OPLS-AA patch for different types of molecules
- Reaction-diffusion systems in 2D space with python
- Constructing discrete Laplacian via sparse matrix
- All-atom automatic OPLS-AA topology generator
- Scanning PES ab initio and in MM
- Quantum chemistry information page
- Python script for processing FRAP image set
- Using Firefly/GAMESS-US efficiently
- Building and plotting Fukui function with FireFly and PyMol
- Visualize partial charges in PyMol
Комментарии
- comcon1 in All-atom automatic OPLS-AA topology…
- zoidberg in Инструкции по уста?…
- Natallia in All-atom automatic OPLS-AA topology…
- » OPLS-AA… in All-atom automatic OPLS-AA topology…
- Luge Zhang in All-atom automatic OPLS-AA topology…
- » Reactio… in Constructing discrete Laplacian via…
- comcon1 in All-atom automatic OPLS-AA topology…
- Luge Zhang in All-atom automatic OPLS-AA topology…
- » Quantum… in Building and plotting Fukui functio…
- » Scannin… in Using Firefly/GAMESS-US efficiently…