Matysiak Silvina, Clementi Cecilia, Praprotnik Matej, Kremer Kurt, Delle Site Luigi
Department of Chemistry, Rice University, Houston, Texas 77005, USA.
J Chem Phys. 2008 Jan 14;128(2):024503. doi: 10.1063/1.2819486.
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS, we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of the here relevant structural, thermodynamical, and dynamical properties, i.e., radial distribution functions, pressure, temperature, and diffusion, of liquid water at ambient conditions.
我们展示了一种采用最近引入的自适应分辨率方案（AdResS）对液态水进行的双分辨率分子动力学（MD）模拟。空间自适应分子分辨率程序允许在飞行中从粗粒度表示切换到全原子表示，反之亦然。为了找到与AdResS一起使用的最合适的粗粒度水模型，我们首先研究不同粗粒度水模型在再现全原子系统结构特性方面的准确性。通常，由于粗粒度时自由度（DOF）的减少，粗粒度分子模型具有比相应全原子模型更高的扩散常数，这消除了与那些被整合掉的分子自由度相关的波动作用力。在这里，我们介绍了在不同分辨率下获得相同扩散动力学的方法。我们表明，这种方法能够正确描述环境条件下液态水在此处相关的结构、热力学和动力学特性，即径向分布函数、压力、温度和扩散。
