Reviewer 4 comments

[labarba]

This paper presents a computational workflow combining a fast multipole method library and a Galerkin boundary element method package for solving the Poisson-Boltzmann (PB) equation for large systems such as viruses. In terms of high-performance, the code is among the best ones of state-of-the-art fast BEM PB solvers. A further special contribution of the workflow is its high-productivity through integrating an easy-to-use and interactive open-sourced platform for coding, computing, and analyzing of FMM BEM PB-type of calculations. These contributions are significant to PB developers community.

Minor comments:

• [x] 1, I suggest the authors provide some description on treating the singularities appeared in surface integrations in the Bempp? The paper only mentioned “The singularity of the Green's function needs to be accounted for in the quadrature rules for integration over adjacent or identical test/trial triangles” on page 10.

• [x] 2, The work only reports the CPU performance of FMM and BEM parts. To give readers more information of a complete BEM calculations, please also provide some CPU info for meshing part, especially for large systems.

• [x] 3, In Figure 4, the unit of potential ?

[labarba]

item 1

I suggest the authors provide some description on treating the singularities appeared in surface integrations in the Bempp? The paper only mentioned “The singularity of the Green's function needs to be accounted for in the quadrature rules for integration over adjacent or identical test/trial triangles” on page 10.

TO-DO: add citation to Erichsen-Sauter 1998, which gives the details for evaluating the integrals as is done in Bempp.

Fixed in: 0b72299

[labarba]

item 2

The work only reports the CPU performance of FMM and BEM parts. To give readers more information of a complete BEM calculations, please also provide some CPU info for meshing part, especially for large systems.

The meshing procedure consisted on running Nanoshaper to generate the mesh, and then deleting any small cavities with a Python script that calls the Trimesh library. The Zika mesh with ~10 million panels took 1m55s to generate in Nanoshaper, and 2m48s to clean with Trimesh, on a 24-core Intel E5-2680 CPU. The script for mesh generation and cleaning is provided in our repro-pack: bempp_exafmm_paper/repro-pack/bempp_pbs/scripts/generate_mesh.py.

• Fixed in 5af2275.

[labarba]

item 3

In Figure 4, the unit of potential ?

Fixed in 2c08b5c and a3f7df0.