Generic Adaptive Resolution Method for Reverse Mapping of Polymers from Coarse-Grained to Atomistic Descriptions

In this paper, we propose a new generic approach for reverse mapping from coarse-grained to atomistic scale based on the adaptive resolution scheme (AdResS). In AdResS simulation, two spatial domains, modeled at two different scales, are brought together in a concurrent simulation by defining a hybr...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2016-11, Vol.12 (11), p.5549-5562
Main Authors: Krajniak, Jakub, Pandiyan, Sudharsan, Nies, Eric, Samaey, Giovanni
Format: Article
Language:English
Subjects:
Computer simulation
Descriptions
Dynamical systems
Mapping
Mathematical analysis
Mathematical models
Melamine
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Summary:In this paper, we propose a new generic approach for reverse mapping from coarse-grained to atomistic scale based on the adaptive resolution scheme (AdResS). In AdResS simulation, two spatial domains, modeled at two different scales, are brought together in a concurrent simulation by defining a hybrid region where particles can switch representation from one model to another. We use AdResS as a central part of a reverse mapping algorithm from a different perspective by treating the whole simulation box as a hybrid region and changing the resolution as a function of time during the course of a molecular dynamics simulation. The proposed method depends only on a single parameter that controls the reverse mapping process and it is independent of atomistic and coarse-grained force-fields. We performed a reverse mapping of three different systems, simple molecules (dodecane), polymer chains (polyethylene) and ring molecules (trimethylol melamine) with a degree of coarse-graining ranging from two to ten heavy atoms. The conformational and dynamical properties of the reconstructed systems are in excellent agreement with the reference atomistic simulation.
ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.6b00595