1. Systems of interest are downloaded from the Protein Data Bank (PDB) server and are prepared for MD simulations using appropriate force field parameters, periodic box vectors, and solvation using the Amber 14 package. 2. Once the system is prepared, it is followed by energy minimization, simulated heating, and equilibration using the OpenMM simulation engine. 3. MD simulation is then performed using the Amber simulation engine for the desired amount of simulation time. Trajectories are saved with the desired frequency.