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Python membrane generator for MD simulations
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. […]
Potential energy surface scanner
This python script is capable of generating a set of GAMESS input files for potential energy surface scanning. It needs a reference GAMESS input and XML file specifying degrees of freedom to scan. PES scan can be done using linear translations, and rotations of atomic groups. Translation vectors can be specified using pair of atoms […]
Normal modes visualization for PyMol
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
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 […]
Visual approach to construction of &QMMM section of CP2K input file
The script is intended to be used from PyMol molecular visualization system and allows one to generate &QM_KIND, &LINK and &CELL parts of CP2K input easily. Given a molecular object name and QM part selection name (which can be defined using either approach available in PyMol) it generates output file with corresponding input groups. To […]
Gaussian Cube files loader
This Python module parses Gaussian cube files, produced by quite a few QM software packages, and makes volume data available as numpy array as well as some associated properties. Look at this example for api reference: Here is the module, save it as «load_cube.py» for use as in the previous example:
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
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