Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations.
| Autor: | Sidler D; Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland., Lehner M; Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland., Frasch S; Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland., Cristófol-Clough M; Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland., Riniker S; Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland. |
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| Jazyk: | angličtina |
| Zdroj: | F1000Research [F1000Res] 2018 Nov 05; Vol. 7, pp. 1745. Date of Electronic Publication: 2018 Nov 05 (Print Publication: 2018). |
| DOI: | 10.12688/f1000research.16715.2 |
| Abstrakt: | 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. Competing Interests: No competing interests were disclosed. |
| Databáze: | MEDLINE |
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