GROMACS produces graphical output in the form of .xvg files. These are designed to be viewed with a classic UNIX/Linux plotting program called Grace. If you happen to be using Linux and you have Grace installed, it is very easy to plot the data with the command xmgrace my_file.xvg
How to plot .xvg files from GROMACS on Windows Read More »
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
Updated GROMACS tutorials Read More »
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.
Finding dimensions of a bounding box in Jmol Read More »