I learned the Molecular Dynamics Simulation process by dealing with the protein Influenza Neuraminidase 3BEQ. Molecular Dynamics Simulation is a multi-step process.
First, I had to visit the protein data bank to download the protein Influenza Neuraminidase and put in a directory on comet. Second, I had to setup the protein in tleap in AMBER. While I set up the protein in tleap, I had to add Ions to the protein and solvate the system with a water box. Third, you have to save the protein in a coordinate and topology file. Fourth, I needed to run energy minimizations using sander in AMBER. Fifth, I then needed to run equilibration. Sixth, I had to run a molecular dynamics run. Seventh, I had to use cpptraj to run a trajectory analysis. Lastly, I used VMD to view the simulation.
The process is tedious and allows a lot of place for error and typos, which could be annoying. Aside for the errors that could take place, the molecular dynamics simulation process is not too bad to handle with guidance.