Ultra-coarse-graining modeling of liquid water
Ultra-coarse-graining modeling of liquid water
复制标题
液态水的超粗粒度建模
DOI：
10.1063/5.0055453
复制
发表时间：
2021-06-14
影响因子：
4.4
通讯作者：
Zhang, John ZengHui
中科院分区：
文献类型：
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作者：
Li, Min;Lu, WenCai;Zhang, John ZengHui
在生物大分子模拟中，建立超粗粒度模型是一个巨大的挑战。在本研究中，我们在之前的工作中提出的原始粗粒度策略[M。李，张建中，物理学。化学。化学。Phys. 23,8926(2021)]首次扩展到液态水的超粗粒化（UCG）模型，N-C从4-10增加到20-500。UCG力场采用自顶向下的方法进行参数化，然后通过试错法对液态水的重要性质进行细化。在N-C = 20/100/500 UCG模拟中，非键相互作用的最佳截止分别由能量收敛决定。结果表明，经过精细化的UCG模型可以准确再现300 K时的平均密度，但在描述压缩系数、自扩散系数等方面存在较大差异。UCG模型预测的密度-温度关系与实验结果吻合较好。此外，在模拟系统平衡后，还观察到UCG分子的两种极化状态。离子参与N-C = 100 UCG模拟得到的离子-水rdf与标度AA模拟结果基本一致。此外，在N-C = 100的模拟中，离子的浓度会影响两个极化态的比值。结果表明，与TIP3P力场相比，UCG模型对液态水的模拟速度提高了114 ~ 135倍。所提出的UCG力场简单、通用、可转移，可能为大型生物分子的UCG模拟提供有价值的信息。
It is a great challenge to develop ultra-coarse-grained models in simulations of biological macromolecules. In this study, the original coarse-graining strategy proposed in our previous work [M. Li and J. Z. H. Zhang, Phys. Chem. Chem. Phys. 23, 8926 (2021)] is first extended to the ultra-coarse-graining (UCG) modeling of liquid water, with the N-C increasing from 4-10 to 20-500. The UCG force field is parameterized by the top-down strategy and subsequently refined on important properties of liquid water by the trial-and-error scheme. The optimal cutoffs for non-bonded interactions in the N-C = 20/100/500 UCG simulations are, respectively, determined on energy convergence. The results show that the average density at 300 K can be accurately reproduced from the well-refined UCG models while it is largely different in describing compressibility, self-diffusion coefficient, etc. The density-temperature relationships predicted by these UCG models are in good agreement with the experiment result. Besides, two polarizable states of the UCG molecules are observed after simulated systems are equilibrated. The ion-water RDFs from the ion-involved N-C = 100 UCG simulation are nearly in accord with the scaled AA ones. Furthermore, the concentration of ions can influence the ratio of two polarizable states in the N-C = 100 simulation. Finally, it is illustrated that the proposed UCG models can accelerate liquid water simulation by 114-135 times, compared with the TIP3P force field. The proposed UCG force field is simple, generic, and transferable, potentially providing valuable information for UCG simulations of large biomolecules.