Applications of Visual Molecular Dynamics Software

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.

Our Services Based on VMD Software

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.

• Explicit Membrane Protein Simulations

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.

• Trajectories Analysis and Movie Making
• Loading trajectories
• Trajectory visualization
• Smoothing trajectories
• Displaying multiple frames
• VMD combined with PyMol software can make trajectory animation after molecular dynamics simulation
• Working with Multiple Molecules
• Loading multiple molecules
• Changing molecule names
• Drawing different representations for different molecules
• Compare Structures and Sequences
• Load aquaporin structure
• Align the molecules
• Coloring molecules by structural properties
• Arrange molecules and color molecules by the degree of conservation
• Molecular Modeling

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.

The Features of VMD Software

• VMD can be used to animate and analyze trajectories of molecular dynamics (MD) simulations.
• VMD can serve as a graphical front-end to external MD programs by displaying and animating the molecule being simulated on a remote computer.
• Supports all major computer platforms
• Supports multi-core processors
• Stereoscopic display capability
• There is no limit to the number of molecules, atoms, residues or trajectory frames, except for available memory
• Many molecular rendering and shading methods
• User-extensible graphical and text-based user interface with built-in standard Tcl/Tk and Python scripting languages
• VMD includes a multiple sequence alignment plugin, a unified bioinformatics analysis environment that allows the organization, visualization, and analysis of sequence and structural data for proteins and nucleic acids.