We simulated a room temperature ionic liquid starting from scratch by “hand-drawing” the molecules with xleap, optimizing the geometry with antechamber, generating the topology and coordinates file with xleap/tleap, and running minimization and MD simulations with sander. We also used ptraj to perform analyses on the data we collected, such as calculating RDFs and self-diffusion coefficients, and we used xmgrace and gnuplot to aid us in visualizing the data. Hopefully, by the end of this tutorial, you'll feel more comfortable with the numerous tools the AMBER suite provides, and you can now move on to more complex simulations (and more complex analyses!).