Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD

Abstract

Computing diffusion coefficients from classical molecular dynamics (MD) simulations is a common task when assessing solvent and lipid dynamics both in bulk and in confined regions. Solute-modulated lateral diffusion of lipids is especially interesting in biological membranes, where it plays a role in receptor activity and raft formation (Dainese et al., 2014). The Diffusion Coefficient Tool is an analysis plugin for the Visual Molecular Dynamics (VMD) analysis environment (Humphrey, Dalke, & Schulten, 1996), which computes various types of diffusion coefficients for a molecular species from simulated trajectories.