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Among other improvements, the Martini 3 coarse-grained force field provides amore accurate description of the solvation of protein pockets and channelsthrough the consistent use of various bead types and sizes. Here, we show thatthe representation of Na$^+$ and Cl$^-$ ions as "tiny" (TQ5) beads limits theaccessible time step to 25 fs. By contrast, with Martini 2, time steps of 30-40fs were possible for lipid bilayer systems without proteins. This limitation isrelevant for, e.g., phase separating lipid mixtures that require longequilibration times. We derive a quantitative kinetic model of time-integrationinstabilities in molecular dynamics (MD) as a function of time step, ionconcentration and mass, system size, and simulation time. With this model, wedemonstrate that ion-water interactions are the main source of instability atphysiological conditions, followed closely by ion-ion interactions. We showthat increasing the ionic masses makes it possible to use time steps up to 40fs with minimal impact on static equilibrium properties and on dynamicalquantities such as lipid and ion diffusion coefficients. Increasing the size ofthe bead representing the ions (and thus changing their hydration) also permitslonger time steps. The use of larger time steps in Martini 3 simulationsresults in a more efficient exploration of configuration space. The kineticmodel of MD simulation crashes can be used to determine the maximum allowedtime step whenever sampling efficiency is critical.

Small ionic radii limit time step in Martini 3 molecular dynamics simulations