VMD Tutorial

The VMD tutorial introduces new users to VMD and its capabilities. It can also be used as a refresher course for the occasional VMD user wishing to employ this program more productively. The tutorial is subdivided into three separate units of increasing complexity. The first unit covers the basics of molecular graphics representations and will introduce everything you need to know to generate nice graphics. The other two units are targeted toward the scientifically-oriented user and focus on scripting in VMD. While scripting may be skipped by the non-technical users, we encourage everyone to give it a try as it provides some very powerful (and easy to use) tools that cannot be offered by a simple graphical user interface.



(html) (pdf, 2.6M) (required tutorial files [.tar.gz, 44.9M], [.zip, 44.9M], individual files)
[VMD Tutorial]

NAMD Tutorial

The NAMD tutorial provides a first introduction to NAMD and its basic capabilities. It can also be used as a refresher course for the non-expert NAMD user. It is subdivided in three sections. The first section covers the basic initial steps of a molecular dynamics simulation, the minimization and equilibration of your system, and describes NAMD's user options and output. The second section introduces typical simulation techniques and the analysis of properties for molecular systems. The third section introduces Steered Molecular Dynamics and the analyis of unfolding pathways of proteins. Finally, descriptions of all files needed for the simulations are provided in the appendices.



(html for Unix/Mac) (pdf for Unix/Mac, 8.0M)
(html for Windows) (pdf for Windows, 6.5M)
(required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms))
[NAMD Tutorial]

Evolution of Biomolecular Structure: Class II tRNA-Synthetases and tRNA

The Evolution of Protein Structure tutorial showcases the new software tools in Multiple Alignment in VMD. Multiple Alignment is an invaluable tool for relating protein structure to its function or misfunction. This tutorial focuses on the examination of the correlation of sequence and structure changes and representing these changes in terms of structural phylogenetic trees.



(pdf, 3.0M) (required tutorial files [.tar.gz, 171M], individual files)
[Evolution of Protein Structure]

Aquaporins with the VMD Multiseq Tool Tutorial

Introduces participants to the VMD MultiSeq Tool, which links protein structures to protein sequences and allows users to compare proteins in terms of structure and sequence. The aquaporin family of membrane proteins, found in a wide range of species including humans, are used for a case study of the applications of the MultiSeq tool. Specifically, the tool is used to conduct a comparative study of the structure and sequence of four aquaporins from different species: human AQP1, bovine AQP1, AqpZ from E.coli, and GlpF (E.coli glycerol facilitator).



(html) (pdf, 1.9M) (required tutorial files [.tar.gz, 248M], individual files)
[Aquaporins with the VMD MultiSeq Tool]

Bioinformatics and Sequence Alignment Tutorial

Bioinformatics uses the statistical analysis of protein sequences and structures to help annotate the genome, to understand their function, and to predict structures when only sequence information is available. Bioinformatics methods are used in fundamental research on theories of evolution and in more practical considerations of protein design. The tutorial begins with classical pairwise sequence alignment methods using the Needleman-Wunsch algorithm, and ends with the multiple sequence alignment available through CLUSTAL W.



(pdf, 1.6M) (required tutorial files [.tar.gz, 570k], individual files)
[Bioinformatics and Sequence Alignment]

Parameterizing a Novel Residue Tutorial

Inevitably there comes a time in any molecular modelling scientist's career when the need to simulate an entirely new molecule or ligand arises. The technique of determining new force field parameters to describe these novel system components therefore becomes an invaluable skill. Determining the correct system parameters to use in conjunction with the chosen force field is only one important aspect of the process. The ability to use several programs simultaneously to examine and refine the system in question is also a critical element of these kinds of problems. This tutorial will walk you through a comprehensive example of how one investigates, sets up, and simulates a small nonstandard ligand bound to a protein system; specifically, we will investigate the glutaminase subunit of the hisH-hisF system and will determine parameters for its covalently bound substrate.



(html) (pdf, 2.5M) (required tutorial files [.tar.gz, 24.2M], [.zip, 24.2M], individual files)
[Parameterixation of a Novel Residue]

Topology File Tutorial

Often, one encounters the need in molecular dynamics to simulate molecules for which topology and parameter information does not exist. In many cases, parameter development is necessary, but in others it may not be. This tutorial introduces how to create this information based on existing topology information for other molecules, without the need for new parameter development. The tutorial is subdivided in three sections. The first one introduces the method of topology file creation and situations when it is appropriate and inappropriate. The second section utilizes the method to create a topology file for a tripeptide bound to an enzyme and performs a simulation of the system. The last section provides the solution to a topology file creation problem posed in the tutorial. A working knowledge of VMD is assumed of those utilizing the tutorial, and later sections assume NAMD has been correctly installed on the user's computer.



(html) (pdf, 4.4M ) (required tutorial files [.tar.gz, 11.2M], [.zip, 11.2M], individual files)
[Topology file tutorial]

Simulation of Water Permeation through Nanotubes Tutorial

In this tutorial, participants will be investigating the permeation of water through nanotubes, as a model for transmembrane permeation of substrates through channels. Participants will observe water movement through an array of nanotubes under two types of simulation conditions, namely, free water diffusion in equilibrium and directional water flow under a hydrostatic pressure difference. Next, participants are taught how to 'decorate' nanotubes using AutoIMD, by modifying and experimenting with charge and charge configurations, and by modifying and experimenting with VdW parameters.



(html) (pdf, 435k) (required tutorial files [.tar.gz, 39.8M], [.zip, 39.8M], individual files)
[Simulation of Water Permeation through Nanotubes]

Stretching Deca-Alanine Tutorial

In this tutorial, participants are introduced to interactive molecular dynamics (IMD) and steered molecular dynamics (SMD) simulations, and to the calculation of potential of mean force (PMF) from trajectories obtained with SMD simulations. One system is used throughout the tutorial: deca-alanine, a peptide composed of ten alanine residues. Deca-alanine is simulated in a vacuum, where it forms an alpha-helix, and using IMD and SMD, participants stretch the molecule by applying an external force, and using SMD trajectories and employing Jarzynski's equality, the PMF involved in the helix-coil transition is calculated.



(html) (pdf, 1.4M) (required tutorial files [.tar.gz, 5.3M], [.zip, 5.3M], individual files)
[Deca-alanine]

VMD Images and Movies Tutorial

The VMD Images and Movies tutorial is designed to give an introduction to advanced techniques for making custom images and movies in VMD. 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. 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. It also shows how to create a movie file from a trajectory using VMD's Movie Maker plugin.



(html) (pdf, [an error occurred while processing this directive]) (required tutorial files [.tar.gz, [an error occurred while processing this directive]], Individual files)
[VMD Images and Movies Tutorial]

User-Defined Forces in NAMD

The Forces tutorial is designed to guide users of VMD and NAMD in the use of the tclForces and tclBC scripts. These script-based facilities simplify the process of adding complex forces to systems and implementing boundary conditions.



(html) (pdf, 4.3M) (required tutorial files [.tar.gz, 306M], Individual files)
[Forces tutorial]

BioNanotechnology Tutorial

This tutorial is designed to guide users of VMD and NAMD in all the steps required to set up a molecular dynamics simulation of a bionanotechnology device. The first unit of the tutorial begins by teaching the user how to build a model of a synthetic device from a crystal unit cell and ends with an ionic current simulation through a nanoscale pore in a synthetic membrane. The second unit guides readers through combining a biomolecule with a synthetic membrane and simulating the resulting system."



(html) (pdf, 2.9M) (required tutorial files [.tar.gz, 189M], Individual files)
[BioNanotechnology tutorial]