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

<p>This data set accompanies the publication "Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations"&nbsp;<br>by Anna M. van Bodegraven, Kevin Focke, Mario Wolter, and Christoph R. Jacob&nbsp;<br>(TU Braunschweig, Germany)&nbsp;</p> <p>It contains the following files:</p> <p><br>Directory '01_AIM':</p> <p>&nbsp; &nbsp; - input (structure.pdb, topol.top and *_input.txt) and results (*.log and<br>&nbsp; &nbsp; &nbsp; Hamiltonian/AtomPos/Dipole/Parameters.txt) from frequency calculations<br>&nbsp; &nbsp; &nbsp; with the Amide-I-maps (AIM) program for six polypeptide test cases<br>&nbsp; &nbsp; &nbsp; (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip), &nbsp; &nbsp;<br>&nbsp; &nbsp; &nbsp; each in vacuo or water with three different maps (Jansen, Skinner,&nbsp;<br>&nbsp; &nbsp; &nbsp; Tokmakoff) for 11 snapshots based on a MD run.<br>&nbsp; &nbsp; To rerun the calculations, you will have to change the paths in&nbsp;<br>&nbsp; &nbsp; the *_input.txt files (topfile, trjfile, sourcedir) accordingly<br>&nbsp; &nbsp;&nbsp;<br>Directory '02_SNF':</p> <p>&nbsp; &nbsp; - results (*.dat, *.out, coord and control) from frequency calculations&nbsp;<br>&nbsp; &nbsp; &nbsp; using Turbomole, SNF, and LocVib for six polypeptide test cases<br>&nbsp; &nbsp; &nbsp; (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip)&nbsp;<br>&nbsp; &nbsp; &nbsp; each in vacuo or water for snapshots based on an MD run.<br>&nbsp; &nbsp; &nbsp;&nbsp;<br>Directory '03_NMA':</p> <p>&nbsp; &nbsp; - coordinates and results from pyADF for NMA molecules each alligned&nbsp;<br>&nbsp; &nbsp; &nbsp; with a peptide bond from the six polypeptide test cases<br>&nbsp; &nbsp; &nbsp; (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip)&nbsp;<br>&nbsp; &nbsp; &nbsp; each in water for 11 snapshots based on a MD run and input&nbsp;<br>&nbsp; &nbsp; &nbsp; (*_input.txt) and results (*.log and Hamiltonian/AtomPos/Dipole/Parameters.txt)&nbsp;<br>&nbsp; &nbsp; &nbsp; from calculations with the Amide-I-maps (AIM) program<br>&nbsp; &nbsp; &nbsp;&nbsp;<br>Directory '04_Handling_Data':</p> <p>&nbsp; &nbsp; - contains all used notebooks to extract the data, plot the figures&nbsp;<br>&nbsp; &nbsp; &nbsp; and calculate the errors<br>&nbsp; &nbsp; - RMSD_Error_vacuo/water.ipynb is used to calculate the overall shifts&nbsp;<br>&nbsp; &nbsp; &nbsp; and generates a map-dependent mean value to shift the frequencies of AIM<br>&nbsp; &nbsp; - Frequencies.ipynb and Couplings.ipynb are used to plot the figures&nbsp;<br>&nbsp; &nbsp; - RMSD_values_vacuo/water.ipynb show the calculations for the statistical&nbsp;<br>&nbsp; &nbsp; &nbsp; analysis<br>&nbsp; &nbsp; To use the notebooks, start with the Dictionary_setup_for_data_for_paper.ipynb&nbsp;<br>&nbsp; &nbsp; to set up the main dictionary from the calculated data</p>