Light Martini water accelerates sampling in coarse-grained molecular dynamics simulations

Abstract

Molecular dynamics (MD) simulations of slow biomolecular processes, such as exploration of the conformational ensembles of intrinsically disordered proteins (IDPs), are computationally demanding. Although coarse-grained (CG) models can substantially speed up the simulations compared to all-atom MD, the sampling challenge can still be significant for large systems and long time scales. Here, we present light Martini water, a low-viscosity water model that accelerates sampling in MD simulations with the Martini CG force field. We systematically reduced the mass of the Martini water beads and verified stable, accurate integration of the equations of motion with 20 fs time steps, as typically used in Martini simulations. Light Martini water has a reduced mass of 20 amu (compared to 72 amu in the standard water model), yielding up to a 2.68-fold increase in the sampling rate of IDP chain reconfiguration in water and a 16 % increase in the lateral diffusion of lipids in a POPC bilayer. Equilibrium properties remained unaffected by the mass scaling, and the speedup was achieved without compromising simulation accuracy. The water model is trivial to implement, has no computational overhead, and should be universally applicable to Martini simulations.