Accurate boundary-integral formulations for the calculation of electrostatic forces with an implicit-solvent model
Codes for paper on different formulations for electrostatics forces calculation with a boundary element method. Collaboration between Ian Addison-Smith, Horacio V. Guzman and Christopher D. Cooper. Here you'll find:
force_simulations.ipynb
,force_plots.ipynb
: Jupyter notebooks files to reproduce the results of the paper. These use the PBJ software: https://github.com/bem4solvation/pbj andpqrs
folder for pqr filesAPBS_script.ipynb
: Jupyter notebook examples for APBS 1.4.1 use for force calculations examplesApbs_simulation.in
,Apbs_template.in
andapbs_tools.py
to run APBS within the jupyter notebookresults
,results_PBJ
: Txt results for simulationsfigures
: Figures obtained in the simulations (Not all were used)msh_sphere
: plots on .msh format for phi, d_phi, P_normal and the force terms in the energy functional variation approach