This archive provides the python scripts required to generate Figs. 5-7 shown in the paper "Interpreting NMR dynamic parameters via the separation of reorientation motion in MD simulation",
by A.A. Smith
Scripts that can be run at the command line: Fig5_ideal_case.py Fig6_fail_ex.py Fig7_corr_fail.py Fig8_methyl_frames.py Fig9_frames2NMR.py
There is NO INSTALLATION required for the code. Just place everything in a folder, navigate there, and run. However, python3 and the following modules must be installed from other sources (these are the tested versions, although other versions may work).
Python v. 3.7.3 numpy v. 1.17.2, scipy v. 1.3.0, pandas v. 0.25.1, MDAnalysis v. 0.19.2, matplotlib v. 3.0.3,
We recommend installing Anaconda: https://docs.continuum.io/anaconda/install/ The Anaconda installation includes Python, numpy, scipy, pandas, and matplotlib. (I also highly recommend using Spyder, which comes with Anaconda, for running the provided scripts interactively, such that one may stop to understand each step in the overall analysis)
MDAnalysis is installed by running: conda config --add channels conda-forge conda install mdanalysis (https://www.mdanalysis.org/pages/installation_quick_start/)
All files are copyrighted under the GNU General Public License. A copy of the license has been provided in the file LICENSE
Copyright 2021 Albert Smith-Penzel