########

This directory contains all the scripts necessary to run the **PET-MAD reference** NpT simulations for solvated alanine dipeptide at varying temperatures.

Running this example requires i-PI installation.

`run_ipi.py` is the main Python script that handles the execution of the MD simulation.

`input.xml` is the xml formatted i-PI input file containing all the specifications for the MD simulation.

`init_strucs` is the directory that contains the 10 starting configuration xyz files.

`petmad_ipi.sh` is the slurm job file that can be queued for the MD simulations.

`create_jobs.sh` is a shell script that creates all jobs at different temperatures, saved under separate sub-directories.

`compute_dihedrals.py` is a support Python script that computes the phi and psi dihedrals of the alanine dipeptide along the trajectory, with details that are specified for this particular MD setup.

`dihedrals.sh` is a shell script that can be executed to compute all the dihedrals.



With the proper set up of the environment, one can do the following:

1. execute `create_jobs.sh` to create all the MD jobs targeting different temperatures.

2. queue all the jobs from the subdirectories.

3. execute `dihedrals.sh` to obtain the dihedral angles used for the Ramachandran plot.

########

