The following data is contained within this entry (as described by folder):
Fmoc-Amino_Acids > contains the trajectories and run files associated with each Fmoc amino acid both in the distinguished by THF content * run (0 – 80), within this are two sub-directories (charged and neutral) which refer to the charge state of the C-terminus in that simulation. System topologies and index files used can be found in the directory box_* (0 – 80) directory. More detail is provided in the README.txt file.
itp_files > Structure files associated with each FmocSAA, as well as the parameter files used for the Martini simulation bead types etc.
scripts > contains all analysis and setup scripts used to generate the simulation structures, exuctue their simulation on the Archie West HPC and analyse the results obtained from the trajectories. Further detail is available in the README.txt file.
structures > these are the relevant *gro and *pdb files used to build the starting structures.
UB_sampling_files > Files used for Umbrella Sampling to determine what bead was best for modelling THF. These were adapted from the Martini tutorial on the same subject which can be found here (http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/partitioning-techniques)