In this section you will learn how to use NAMD to set up basic molecular dynamics (MD) simulations. You will learn about typical NAMD input and output files, in particular, those for protein energy minimization and equilibration in water.
NOTE: You will be generating output data in this section by performing simulations and using other features of NAMD. These files are needed for Units 2 and 3. If you are not able to produce the output, correct versions have been provided for each section and may be found in the example-output folder inside the directory corresponding to the given simulation or exercise.