Search Results for "vmd"
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Showing 9 open source projects for "vmd"
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BFEER
Binding Free Energy EstimatoR (BFEER): A VMD plugin for MMPBSA and LIE
BFEER is an open-source GUI-based VMD Plugin for estimating free energy using popular endpoint methods like MMPBSA and LIE. It is designed to work with NAMD's DCD-PSF files. -
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Jmol
An interactive viewer for three-dimensional chemical structures.
...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. ...">
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vmdStore
vmdStore provides a user-friendly interface to free install VMD plugin
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">
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MEMBPLUGIN
MEMBPLUGIN: studying membrane complexity in VMD
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. -
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Truncate Trajectory (VMD plugin)
reduces the size of MD trajectories
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... -
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birgHPCC
Rapid CUDA Cluster Deployment
...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. -
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MIPGen
Simple Molecular Interaction Potential Generator in Python
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). -
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Jedná se o open-source překlad sedmého vydání knihy Organic Chemistry od Johna McMurryho. Překlad je tvořen v LaTeXu, veškerá grafika bude vytvořena v open-source nástrojích jako je GIMP, InkSpace, xmGrace, VMD či TurboMole.
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It is transparent command prompt for windows. Unlike other similar transparent command prompt which uses simple opacity property to enable transparency. this vmd (vista style command prompt) provide 100% transparency without blurring of text.
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