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A general-purpose coarse-grained molecular dynamics program

机译：通用的粗粒度分子动力学程序

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摘要

In this article, we describe a general-purpose coarse-grained molecular dynamics program COGNAC (COarse Grained molecular dynamics program by NAgoya Cooperation). COGNAC has been developed for general molecular dynamics simulation, especially for coarse-grained polymer chain models. COGNAC can deal with general molecular models, in which each molecule consists of coarse-grained atomic units connected by chemical bonds. The chemical bonds are specified by bonding potentials for the stretching, bending and twisting of the bonds, each of which are the functions of the position coordinates of the two, three and four atomic units. COGNAC can deal with both isotropic and anisotropic interactions between the non-bonded atomic units. As an example, the Gay-Berne potential is implemented. New potential functions can be added to the list of existing potential functions by users. COGNAC can do simulations for various situations such as under constant temperature, under constant pressure, under shear and elongational deformation, etc. Some new methods are implemented in COGNAC for modeling multiphase structures of polymer blends and block copolymers. A density biased Monte Carlo method and a density biased potential method can generate equilibrium chain configurations from the results of the self-consistent field calculations. Staggered reflective boundary conditions can generate interfacial structures with smaller system size compared with those of periodic boundary conditions.
机译：在本文中，我们描述了通用的粗粒度分子动力学程序COGNAC（名古屋合作社的粗粒度分子动力学程序）。 COGNAC已开发用于一般分子动力学仿真，尤其是用于粗粒聚合物链模型。 COGNAC可以处理一般的分子模型，其中每个分子由通过化学键连接的粗粒度原子单元组成。化学键是通过键的拉伸，弯曲和扭曲的键电位来指定的，每个键都是两个，三个和四个原子单元的位置坐标的函数。 COGNAC可以处理非键合原子单元之间的各向同性和各向异性相互作用。例如，实现了盖伊-伯恩势。用户可以将新的潜在功能添加到现有潜在功能列表中。 COGNAC可以对各种情况进行仿真，例如在恒温，恒压，剪切和伸长变形等条件下。COGNAC中采用了一些新方法来模拟聚合物共混物和嵌段共聚物的多相结构。密度偏置的蒙特卡洛方法和密度偏置的势方法可以根据自洽场计算的结果生成平衡链构型。与周期性边界条件相比，交错的反射边界条件可以生成具有较小系统尺寸的界面结构。

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