Data Set "Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations"

This data set accompanies the publication "Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations" by Anna M. van Bodegraven, Kevin Focke, Mario Wolter, and Christoph R. Jacob (TU Braunschweig, Germany) It contains the following files: Directory 'AIM': - input (structure.pdb and *_input.txt) and results (*.log and Hamiltonian/AtomPos/Dipole/Parameters.txt) from frequency calculations with the Amide-I-maps (AIM) program for six polypeptide test cases (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip), each in vacuo or water with three different maps (Jansen, Skinner, Tokmakoff) for 11 snapshots based on a MD run. - the used topology files for vacuo calculation are at the top level for each structure. For the water calculations, they are within the folder for the respective snapshot. - to rerun the calculations, you will have to change the paths in the *_input.txt files (topfile, trjfile, sourcedir) accordingly Directory 'SNF': - results (*.dat, *.out, coord and control) from frequency calculations using Turbomole, SNF, and LocVib for six polypeptide test cases (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip) each in vacuo or water for 11 snapshots based on a MD run. Directory 'Handling_Data': - contains all used notebooks to extract the data, plot the figures and calculate the errors - to use the notebooks, start with the Dictionary_setup_for_data_for_paper.ipynb to set up the main dictionary from the calculated data - the RMSD_Error_vacuo/water.ipynb is used to calculate the overall shifts and generates a map-dependent mean value to shift the frequencies of AIM - Frequencies.ipynb and Couplings.ipynb are used to plot the figures - RMSD_values_vacuo/water.ipynb show the calculations for the statistical analysis