STRD MARTINI: Simulating Quasi-2D Hydrodynamics with Chemically Detailed Lipid Models

Abstract

Hydrodynamic interactions are an important component of lipid membrane dynamics. A proper molecular dynamics simulation of lateral diffusion in a membrane requires coupling to hydrodynamic flows in the surrounding solvent. In the low Reynolds number limit, the interactions mediated by these flows are long-ranged. Camley, et al recently generalized the Saffman-Delbruck result to periodic boundary conditions, and showed that hydrodynamic interactions introduce significant error into lateral diffusion of lipids and proteins in typical molecular dynamics simulations. The system sizes required to overcome the finite size effect are computationally prohibitive when using explicit solvent models in both all-atom and coarse-grained simulation. Implicit solvent models offer a potential solution, but entirely neglect hydrodynamic momentum transport. To remedy this, we have supplemented the Dry MARTINI implicit solvent model with an efficient mesoscopic particle-based hydrodynamic model called Stochastic Rotation Dynamics (SRD). Our implementation allows for fine control over fluid properties of the solvent, such as viscosity and Reynolds number, and includes a thermostat for the solvent that produces canonical energy fluctuations without interfering with the mesoscopic hydrodynamic flows. The approach, dubbed “STRD Martini”, has been implemented in an in-house version of Gromacs v 5.1.