Adaptive Boundaries in Multiscale Simulations

Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of d...

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Bibliographic Details
Published in:arXiv.org 2018-04
Main Authors: Wagoner, Jason A, Pande, Vijay S
Format: Article
Language:English
Subjects:
Algorithms
Boundaries
Computer simulation
Distribution functions
Simulation
Online Access:Get full text
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Summary:Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of degrees of freedom required to accurately represent even a simple molecular process can vary by several orders of magnitude throughout the course of a simulation, and adaptive boundaries react to these changes to include an appropriate but not excessive amount of detail. Here, we derive the Hamiltonian and distribution function for such a molecular simulation. We also design an algorithm that can efficiently sample the boundary as a new coordinate of the system. We apply this framework to a mixed explicit/continuum representation of a peptide in solvent. We use this example to discuss the conditions necessary for a successful implementation of adaptive boundaries that is both efficient and accurate in reproducing molecular properties.
ISSN:2331-8422
DOI:10.48550/arxiv.1802.05555