Analysis of the Electrostatic Forces between an AFM tip and a virus capsid from PB simulations

Paper on Quantitative electrostatic force tomography for virus capsids in interaction with an approaching nanoscale probe. Collaboration between Christopher D. Cooper, Ian Addison-Smith and Horacio V. Guzman. Before running the jupyter notebooks, the following files are required:

• ZIKV_6CO8_aa_charge_vdw_addspace.pqr
• surf_gs1.0_noTER_split.face and surf_gs1.0_noTER_split.vert
• phi.txt and dphir.txt data from simulations in Pygbe, for distances 2, 4, 6, 8, 10, 12, 14, 16, 20, 50, 100, 500, 1000 Angstrom between capsid and tip

Here you'll find:

• Force_components_afmtip.ipynb : Jupyter notebook script to get force qf, db, ib components plotted between several distances between capsid and tip
• Forcesqf_afmtip.ipynb : Jupyter notebook script to get force qf component plotted between several aminoacid in slices of capsid
• generate_vtk_afmtip.py: Python script which generate the .vtk file who visualize the boundary forces on capsid surface