Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water.

ABSTRACT: The need for short time steps currently limits routine atomistic molecular dynamics (MD) simulations to the microsecond time scale. For long time steps, the numerical integration of the equations of motion becomes unstable, resulting in catastrophic crashes. Here, we combine mass repartitioning and rescaling to construct a water model that increases the sampling efficiency in biomolecular simulations without compromising integration stability and with preserved structural and thermodynamic properties. The resulting "fast water" is then used with a time step as before in combination with standard force fields. The reduced water viscosity and faster diffusion result in proportionally faster sampling of the larger-scale motions in the conformation space of both solute and solvent. We illustra

SUBMITTER: Rosas Jimenez JG 

PROVIDER: S-EPMC11672673 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature