Abstract
Background:Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts.Methods:The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution.Results:In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces. The presence of the observed artefacts was found to be independent of the interface shape and the thermostatting method used. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs.Conclusion:A SR scheme avoids numerical artefacts and offers an interesting alternative to TR RESPA with respect to performance optimization.
Highlights
To describe the dynamic processes of biomolecules, such as proteins, DNA, carbohydrates and membranes, molecular dynamics (MD) simulations have been proven to be a powerful technique to provide insights at the atomic level
The minor differences between SR schemes with different update frequencies can only be seen in density difference plots (Figure 4) with respect to the SR reference run (n = n = 1). These findings indicate that the observed density increase is mainly caused by resonance artefacts due to the constant mid-range forces application (CFA) multiple time-step (MTS) integration
The effect of using the TR scheme with a constant force application (CFA) at solvent-solvent interfaces was investigated with layer and droplet systems of different composition
Summary
To describe the dynamic processes of biomolecules, such as proteins, DNA, carbohydrates and membranes, molecular dynamics (MD) simulations have been proven to be a powerful technique to provide insights at the atomic level. Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple timestep integration methods are often employed to increase the speed of MD simulations. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Conclusion: A SR scheme avoids numerical artefacts and offers an interesting alternative to TR RESPA with respect to performance optimization
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