Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0]

This LiveCoMS document is maintained online on GitHub at https: //github.com/delphi001/ delphi_tutorial_livecoms; to provide feedback, suggestions, or help improve it, please visit the GitHub repository and participate via the issue tracker. This version dated November 25, 2019 Abstract Electrostatics play an indispensable role in practically any process in molecular biology. Indeed, at distances larger than several Angstroms, all other forces are negligibly small and electrostatic force dominates. However, modeling electrostatics in molecular biology is a complicated task due to presence of water phase, mobile ions and irregularly shaped inhomogeneous biological macromolecules. A particular approach to calculating electrostatics in such systems is to apply the Poisson-Boltzmann equation (PBE). Here, we provide a tutorial for the popular DelPhi package that solves PBE using a finite-difference method and delivers the electrostatic potential distribution throughout the modeling box. The tutorial comes with a detailed description of different tasks that DelPhi can handle, an assessment of the accuracy against cases with analytical solutions and recommendations about DelPhi usage. Furthermore, since electrostatics is a key component of virtually any modeling in molecular biology, we have created many additional resources utilizing DelPhi to model various biology relevant quantities. Tutorials for these resources are also provided along with examples of their usage.