Coloring molecules by electrostatic potential, and other volumetric data.Creating interactive 3-D PDF documents with VMD and Acrobat3D.VMD outline rendering style inspired by the work of D.Publication figure rendering using NVIDIA Gelato.Publication figure rendering with Tachyon.Short and topical VMD tutorials: Preparing large MD simulations with VMD.*Note: download of files may be limited by bandwidth availability. This tutorial will demonstrate how to use features in NAMD and VMD to harness the computational power of graphics processing units (GPUs) to accelerate simulation, visualization and analysis. GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis ( pdf, 443K) ( required tutorial files *).In this tutorial output from the GAMESS program will be used to provide input for visualization of QM Data using VMD. With QM data loaded, VMD can display molecular orbitals, as well as access the calculated energy levels and various other data present in the loaded files. VMD can be used to load files that contain quantum mechanics (QM) data such as GAMESS log files and Molden files. VMD Quantum Chemistry Visualization Tutorial ( pdf, 2.0M) (required tutorial files, individual files).Tutorial works on Windows, Mac, and Unix/Linux platforms. The plugins can also be used to prevent these errors from occuring in simulations with NAMD.

This tutorial describes two VMD plugins that can be used to detect and correct certain structure errors, namely chirality and cis peptide bonds. Structure Check ( html) ( pdf, 720k) (required tutorial files, individual files).It also shows how to create a movie file from a trajectory using VMD's Movie Maker plugin. The second part demonstrates how to work with trajectories, by using techniques such as smoothing trajectories, showing multiple frames at once, and making atom selections 'follow' a trajectory. The first section looks at how to use features such as resolution, color, and material, depth perception, and volumetric data to produce effects and enhancements for still images. This tutorial is designed to give users of VMD an introduction to advanced techniques for making custom images and movies. VMD Images and Movies Tutorial ( html) ( pdf, 26.1M) ( required tutorial files, , individual files).The previous version of the tutorial can be found here. Additionally, participants learn how to look for interesting structural properties of proteins using VMD. Participants build an image of ubiquitin while becoming familiar with basic VMD commands. Using VMD ( html) ( pdf, 1.4M) ( required tutorial files, , individual files).

Be sure you have the latest version of VMD. The tutorials below focus on VMD-specific features, although many other tutorials utilize VMD as well.

Vmd commands