(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015

TUTORIAL B2

Using VMD with AMBER

By Ross Walker

Updated for VMD 1.9.2
[by Aditi Munshi and Ross Walker]

This tutorial is designed to give you an introduction to using VMD with AMBER, covering how to load AMBER trajectory files and inpcrd files and then how to manipulate the data. It is not designed to exhaustively cover all of the many features that are present in VMD.

Introduction

Visual Molecular Dynamics (VMD), available at http://www.ks.uiuc.edu/Research/vmd/, is a very powerful and feature rich molecular visualization package for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Its development is funded by the National Institute of Health under the guidance of Klaus Schulten. It is available free of charge to academic researchers and can be downloaded from the above link after registering.

VMD is an ideal tool for visualizing results produced by the pmemd module of the AMBER software suite. However, its use is not necessarily intuitive. This tutorial is designed therefore to give a brief introduction to visualizing and manipulating trajectories produced from AMBER simulations.

This tutorial is based on VMD v1.8.3 which at the time of writing (3rd June 2005) was the most up to date version. It has been updated for VMD v1.9.2. If you use a different version of VMD you may find that some features are not available or the interface is slightly different. However, it should still be possible to complete the vast majority of this tutorial.

This tutorial also assumes that you are using Linux. If your operating system is different some of the layout and/or procedures may be slightly different.

This tutorial consists of  nine sections:

  1. section1.htm : Loading VMD and Customizing the Initial Window Layout

  2. section2.htm : Loading a PDB File

  3. section3.htm : Changing Representations

  4. section4.htm : Loading AMBER inpcrd and restrt files

  5. section5.htm : Aligning Molecules and Measuring RMSD's

  6. section6.htm : Visualizing AMBER Trajectories

  7. section7.htm : Saving a Single Set of Coordinates

  8. section8.htm : Following System Parameters Over the Course of a Trajectory

  9. section9.htm : Creating a Movie


CLICK HERE TO GO TO SECTION 1


(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015