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 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.
Department of Computer Science, KU Leuven , Celestijnenlaan 200A, 3001 Leuven, Belgium.
Jakub
J
Krajniak
Division of Polymer Chemistry and Materials, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium.
Sudharsan
S
Pandiyan
Division of Polymer Chemistry and Materials, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium.
Eric
E
Nies
Department of Computer Science, KU Leuven , Celestijnenlaan 200A, 3001 Leuven, Belgium.
Giovanni
G
Samaey