Search Results for "vmd"

...Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. ...

vmdStore provides a user-friendly interface to free install VMD plugins. vmdStore also helps you keeping the plugins always updated. Minimum Requirements Operating System: macOS, Linux, or Windows Visual Molecular Dynamics (VMD) 1.9.3 or later

MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers.

Large trajectories have a lot of redundant hetero compounds which augment their size and render calculations cumbersome. Truncate Trajectory is designed to help you discard these compounds. It currently works only with parallelepiped unit cells and periodic boundary conditions, as it is able to detect periodic contacts with hetero compounds from the 26 nearest cells, and incorporates these compounds to the final trajectory. The dimensions and angles (a, b, c, alpha, beta, and gamma) should...

...In addition to the increase in image size (less than 2 gigabytes) and a new Linux base (previously Debian, now Ubuntu), CUDA-capable bioinformatics software programs, such as NAMD, HOOMD-blue, VMD, GPU-HMMER and GPU-BLAST, are pre-installed in birgHPCC, along with the CUDA driver, libraries and software development kit (SDK). In short, birgHPCC is the world's first CUDA-ready, bioinformatics-based, live DVD.

Molecular Interaction Potential Generator MIPGEN is a python program that will calculate Molecular Interaction Potential grids over a given molecule, that could be either a protein or a small organic compound (drug). The output will be a series of grids with DX format (*.dx) that the user will be able to visualize using any Molecular visualization program like VMD, PyMol, Chimera... For more information on dependencies and usage, please read the Documentation. Users are welcome to post any bug or request under BUGS & REQUESTS menu. (sourceforge account will be needed).