Visual Molecular Dynamics (VMD) is a suite of molecular modeling and visualization software developed by the Theoretical and Computational Biophysics Group for analyzing experimental data from molecular dynamics simulations. At the same time, the software also includes modules for processing length and reference-related data, which can visualize and analyze trajectories, add arbitrary graphics, and export to formats that other software can use, such as POV-Ray, PRMan, VRML, etc. VMD can be used in Unix, it runs under operating systems such as MacOS and Microsoft Windows. VMD is designed to model, visualize, and analyze biological systems such as proteins, nucleic acids, lipid bilayer assemblies, and more. It can be used to view more general molecules because VMD can read standard Protein Data Bank (PDB) files and display the structures contained. VMD provides a variety of ways to render and color molecules: simple points and lines, CPK spheres and cylinders, licorice bonds, skeleton tubes and ribbons, cartoons, and more.
CD ComputaBio employs state-of-the-art molecular modeling, bioinformatics and computational techniques to solve biomedical related problems. We extend, improve and deliver these technologies in response to experimental advances and emerging needs of the broad biomedical research community. On the VMD software platform, CD ComputaBio can provide customers with high-quality computational biology services.
We can use VMD display to analyze biological macromolecules such as protein, nucleic acid, lipid bilayer assembly, and perform 3D structure display, highlight important parts of the molecule, add labels, perform molecular docking and molecular dynamics simulations, etc.
Scientists at CD ComputaBio use the psfgen plugin to generate rtf files (or inp files) under the CHARMM force field, and use patches to process connections between residues or residue ends for molecular modeling.