Author:

Keywords:

Science & Technology, Physical Sciences, Chemistry, Physical, Physics, Atomic, Molecular & Chemical, Chemistry, Physics, MOLECULAR-DYNAMICS, FORCE-FIELD, MONTE-CARLO, INTERACTION POTENTIALS, MECHANICAL-PROPERTIES, SIMULATIONS, MODELS, MELTS, EFFICIENT, LANGEVIN, 0307 Theoretical and Computational Chemistry, 0601 Biochemistry and Cell Biology, 0803 Computer Software, Chemical Physics, 3406 Physical chemistry, 3407 Theoretical and computational chemistry

Abstract:

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.