Simulation output

Again, depending on whether or not Espresso is used, there will be two distinct ways the program will run. However, the output in both cases are mainly the same. The purpose of the script is to build a peptide and output the coordinates in a .pdb file (plus a .psf file for the structure).

• Espresso turned off : only one pdb file will be created. This will correspond to the geometry of the peptide freshly built.
• Espresso turned on : there will be as many pdb files as the variable $int_n_times. Between two pdb files, Espresso will have integrated the equations of motion $int_steps times. This can all be parametrized in a given configuration file.

All the ouput files are stored in the folder $directory.