I have published up-to-date versions of two classic GROMACS tutorials on GitHub. The Getting Started section of the GROMACS online documentation contains some helpful tutorials.  Unfortunately, these tutorials have not been updated in a while. They also don’t explain how to set up an efficient workflow to run large molecular dynamics simulations on a shared cluster using a resource manager such at Torque. I have created a set of files that implement the speptide tutorial from the GROMACS documentation.You can use my files and follow along with the explanations in the GROMACS manual. Continue reading →

The Jmol applet (or Java application) is widely used to visualize the structure of molecules.  It is very powerful, but not that well documented. If you don’t have Jmol running, open the page for Glucose Oxidase (1CF3) from the Protein Databank so you can follow the instructions for finding the size of the bounding box. Right-click on the applet to get a pop-up menu with lots of options.  Continue reading →