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 for weak coupling and Nosé-Hoover (chain) thermostats. 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 or a stochastic dynamics thermostat, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion:TR schemes are not advisable to use in combination with weak coupling or Nosé-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces.
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
These findings indicate that the observed density increase among non-stochastic thermostats is mainly caused by resonance artefacts due to the constant mid-range forces application (CFA) multiple time-step (MTS) integration
It could be shown that the presence of the artificial density increase at the interfaces is independent of the interface geometry as well as the chemical composition of the system the magnitude could vary
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: TR schemes are not advisable to use in combination with weak coupling or Nosé-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces
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