Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations.

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 inves

SUBMITTER: Sidler D 

PROVIDER: S-EPMC6441880 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature