Quantifying electrostatics from (bio)molecular dynamics trajectories using g-elpot

Abstract

Electrostatics plays a pivotal role in many physiological processes, defining ion selectivity of ion channels, driving formation of supramolecular complexes, and determining energetics of transmembrane transporters, to name a few. Atomistic molecular dynamics (MD) simulations can serve as a rich source of structural and dynamic information on such processes. However, tools for robust high-resolution quantification of biomolecular electrostatics from MD trajectories are still limited. Here we present g_elpot, a GROMACS-based tool for calculating electrostatic potentials from MD simulations using the Smooth Particle Mesh Ewald (SPME) method.