Molecular Dynamics Properties without the Full Trajectory: A Denoising Autoencoder Network for Properties of Simple Liquids
Molecular Dynamics Properties without the Full Trajectory: A Denoising Autoencoder Network for Properties of Simple Liquids
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DOI：
10.1021/acs.jpclett.9b02820
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发表时间：
2019-12-19
影响因子：
5.7
通讯作者：
Aluru, N. R.
中科院分区：
文献类型：
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作者：
Moradzadeh, Alireza;Aluru, N. R.
分子动力学（MD）模拟是一种广泛使用的计算工具，用于计算各种系统（包括液体、固体、生物系统等）的微观和宏观性质。为了以最小的噪声或波动确定原子系统的性质，MD模拟在从几纳秒到几十到几百纳秒的范围内的长时间内执行，这取决于系统和设备。感兴趣的属性。在这项研究中，通过考虑简单的液体，我们探讨了显着减少MD模拟时间来计算单原子系统的各种属性，如结构，压力和等温压缩性的可行性。为了做到这一点，在12 000个不同的Lennard-Jones系统在各种热力学状态下进行了广泛的MD模拟。然后，训练深度去噪自动编码器网络，从Lennard-Jones液体的单个快照中获取径向分布函数（RDF），以计算平均时间平均RDF。我们表明，该方法是成功的预测RDF和其他属性，如压力和等温压缩性，可以计算的基础上RDF不仅为Lennard-Jones液体在各种热力学状态，但也为各种简单的液体所描述的指数，汤川，和逆幂律对潜力。
Molecular dynamics (MD) simulation is a popularly used computational tool to compute microscopic and macroscopic properties of a variety of systems including liquids, solids, biological systems, etc. To determine properties of atomic systems to a good level of accuracy with minimal noise or fluctuation, MD simulations are performed over a long time ranging from a few nanoseconds to several tens to hundreds of nanoseconds depending on the system and the properties of interest. In this study, by considering simple liquids, we explore the feasibility of significantly reducing the MD simulation time to compute various properties of monatomic systems such as the structure, pressure, and isothermal compressibility. To do so, extensive MD simulations are performed on 12 000 distinct Lennard-Jones systems at various thermodynamic states. Then, a deep denoising autoencoder network is trained to take the radial distribution function (RDF) from a single snapshot of a Lennard-Jones liquid to compute the mean, temporally averaged RDF. We show that the method is successful in the prediction of RDF and other properties such as the pressure and isothermal compressibility that can be computed based on the RDF not only for Lennard-Jones liquids at various thermodynamic states but also for various simple liquids described by exponential, Yukawa, and inverse-power-law pair potentials.