Calculates 3d structure factor and simulated x-ray diffraction pattern from molecular dynamics trajectories

• scipy
• mayavi
• tqdm
• MDAnalysis
• duecredit
• mdtraj
• pandas
• future
• setuptools
• wheel
• vtk

pip install --upgrade pip                                                   
pip install cython                                                          
pip install vtk                                                             
pip install pandas                                                          
pip install -r requirements.txt

example program usage:

main_gromacs.py -i foo    

(loads foo.gro and foo.trr)

main_gromacs.py -top foo.gro -traj foo.trr

The program will then create two intermediate files, out_foo_traj.npz and out_foo_sf.npz. On subsequent runs of the program with the same inputs, these files will be automatically reloaded.

Output:

The program will create a folder foo_plots, which will contain subfolders with various cross sections through the 3d structure factor. Additionally, Ewald-corrected plots will be produced. These more accurately show what would be seen in an x-ray diffraction experiment.

Coscia, B. J., Yelk, J., Glaser, M. A., Gin, D. L., Feng, X., & Shirts, M. R. (2019). Understanding the Nanoscale Structure of Inverted Hexagonal Phase Lyotropic Liquid Crystal Polymer Membranes. Journal of Physical Chemistry B, 123(1), 289–309. https://doi.org/10.1021/acs.jpcb.8b09944