Abstract: We present the implementation of a computer simulation laboratory for the calculation of the heat capacity of the folding-unfolding pseudo phase transition of a polyalanine Ala30α-helix, using molecular dynamics simulations. Unlike conventional calorimetry experiments, which provide a macroscopic interpretation of the heat capacity, the computer laboratory additionally offers a molecular perspective of the energy exchange processes that lead to the peak of the heat capacity at the phase transition, as well as the statistical mechanical interpretation of the phase transition. The exercise is targeted toward 1st- or 2nd-year students of biophysics in the context of an undergraduate physical chemistry course. We use a graphical web interface to overcome the steep learning barriers associated with command line interactions in commonly used molecular dynamics protocols. The web interface (VIKING) also handles communication with computing hardware in the background, so that students with limited or no programming experience can launch and analyze the simulations easily. A collaboration between the VIKING support team and responsible teachers is required to set up VIKING. We also present a solution in which simulations can be launched on students’ own computers, if some command line knowledge can be expected. The laboratory can also be repurposed for students of various backgrounds (physics, chemistry, biology, or engineering) and scholastic levels (undergraduate or graduate). URL