Normal modes describe the vibrations of different molecular compounds. Analyzing these different modes can be done through the use of VMD and ProDy.
You can think of normal modes through the act of breathing. There are a lot of different movements involved in the act of breathing. For example, your lungs expand, your diaphragm moves down, and your mouth opens wide. Each of these motions have a different contribution to the act of you breathing. The most dominant, your lungs expanding, would be the primary mode (mode 1)–it’s the biggest contributor to the act of breathing. The other motions are different modes (e.g., mode 2 or mode 3). You can break down breathing into hundreds or thousands of motions, but after those first few major ones, there’s not much else that’s important (i.e., any movement to your left pinky toe when you breathe probably isn’t relevant).