Simulating a polypeptide with GROMACS

1The main assignment¶

Perform all-atom molecular dynamics simulations of an aqueous solution of a poly-alanine with an a-helix conformation at $T = 290$ K using the CHARMM force field. In the work you should:

1. Use the minimized structure (mini.gro) of an aqueous solution of poly-alanine equilibrate the system in temperature ($T = 290$ K) and pressure ($P = 1$ bar), following a procedure similar to what was done at $T = 350$ K during the tutorial. You should plot the time evolution of the temperature during the $NVT$ simulation, and as well as the time evolution of the density during the $NPT$ simulation to check the system equilibration.
2. Run 10 ns of simulation at 290 K and check the temperature and density during the data acquisition.
3. Calculate the root mean-squared deviation and the radius of gyration of the poly-alanine as a function of time and compare it to the behavior observed at 350 K and discuss the plot.

2Additional details¶

The files required to run the simulation, together with some instructions about how to install VMD and GROMACS, can be found at this link. Use the slides presented during the tutorial (which can be found in the “Diario delle lezioni” section) to guide you through the procedures required to run the simulations. Note that you have to be logged in as a Sapienza user to be able to access the two files.