Program is compiled as: python fluxionalize.py -p [number of processsors, default 2] -n [name, default "test"] -l [location, default current working directory] -c [number of clusters saved in [name]_out, default 1] -i [input]

Input is given as -i '[SMILES string]' or -i [file], requiring quotation marks for the SMILES string input to avoid bash syntax error

When the calculation has completed, the following files/directories will have been generated in the specified/default location: [name]_out contains the conformer pdb files for each instance [name].out the logfile from the queue containing all the runtime command line outputs [name].tar.gz contains all the files used and generated by the work flow, compressed for space

All of the files in this repository besides fluxionalize.py and flux.py should be saved in a src_files directory. If another directory is used, then that location will have to be changed in flux.py.

Files to Edit: mol_cluster files the catdcd location will have to be specified (line 5)

Files to Check: fluxionalize.py check modules: intel64 (line 49), openmpi (line 50). check version: namd (line 53) flux.py check mpirun location (line 165), set to default