Krajniak Jakub, Pandiyan Sudharsan, Nies Eric, Samaey Giovanni
Department of Computer Science, KU Leuven , Celestijnenlaan 200A, 3001 Leuven, Belgium.
Division of Polymer Chemistry and Materials, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium.
J Chem Theory Comput. 2016 Nov 8;12(11):5549-5562. doi: 10.1021/acs.jctc.6b00595. Epub 2016 Oct 19.
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.
在本文中，我们基于自适应分辨率方案（AdResS）提出了一种从粗粒化尺度到原子尺度的反向映射新通用方法。在AdResS模拟中，通过定义一个混合区域将两个以不同尺度建模的空间域结合在一个并发模拟中，在该混合区域中粒子可以从一种模型切换到另一种模型表示。我们从不同角度将AdResS用作反向映射算法的核心部分，将整个模拟盒视为一个混合区域，并在分子动力学模拟过程中根据时间改变分辨率。所提出的方法仅依赖于一个控制反向映射过程的单一参数，并且与原子力场和粗粒化力场无关。我们对三个不同系统进行了反向映射，包括简单分子（十二烷）、聚合物链（聚乙烯）和环状分子（三羟甲基三聚氰胺），粗粒化程度范围为2到10个重原子。重建系统的构象和动力学性质与参考原子模拟结果非常吻合。
