Kubincová Alžbeta, Riniker Sereina, Hünenberger Philippe H
Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland.
J Chem Phys. 2021 Sep 7;155(9):094107. doi: 10.1063/5.0057384.
A new approach termed Adaptive Solvent-Scaling (AdSoS) is introduced for performing simulations of a solute embedded in a fine-grained (FG) solvent region itself surrounded by a coarse-grained (CG) solvent region, with a continuous FG ↔ CG switching of the solvent resolution across a buffer layer. Instead of relying on a distinct CG solvent model, the AdSoS scheme is based on CG models defined by a dimensional scaling of the FG solvent by a factor s, accompanied by an s-dependent modulation of the atomic masses and interaction parameters. The latter changes are designed to achieve an isomorphism between the dynamics of the FG and CG models, and to preserve the dispersive and dielectric solvation properties of the solvent with respect to a solute at FG resolution. This scaling approach offers a number of advantages compared to traditional coarse-graining: (i) the CG parameters are immediately related to those of the FG model (no need to parameterize a distinct CG model); (ii) nearly ideal mixing is expected for CG variants with similar s-values (ideal mixing holding in the limit of identical s-values); (iii) the solvent relaxation timescales should be preserved (no dynamical acceleration typical for coarse-graining); (iv) the graining level N (number of FG molecules represented by one CG molecule) can be chosen arbitrarily (in particular, N = s is not necessarily an integer); and (v) in an adaptive-resolution scheme, this level can be varied continuously as a function of the position (without requiring a bundling mechanism), and this variation occurs at a constant number of particles per molecule (no occurrence of fractional degrees of freedom in the buffer layer). By construction, the AdSoS scheme minimizes the thermodynamic mismatch between the different regions of the adaptive-resolution system, leading to a nearly homogeneous scaled solvent density sρ. Residual density artifacts in and at the surface of the boundary layer can easily be corrected by means of a grid-based biasing potential constructed in a preliminary pure-solvent simulation. This article introduces the AdSoS scheme and provides an initial application to pure atomic liquids (no solute) with Lennard-Jones plus Coulomb interactions in a slab geometry.
一种称为自适应溶剂缩放（AdSoS）的新方法被引入，用于对嵌入在细粒度（FG）溶剂区域且该区域本身又被粗粒度（CG）溶剂区域包围的溶质进行模拟，溶剂分辨率在缓冲层上实现从FG到CG的连续切换。AdSoS方案并非依赖于独特的CG溶剂模型，而是基于通过因子s对FG溶剂进行维度缩放定义的CG模型，同时伴随着与s相关的原子质量和相互作用参数的调制。后一种变化旨在实现FG和CG模型动力学之间的同构，并在FG分辨率下保持溶剂相对于溶质的色散和介电溶剂化性质。与传统粗粒度方法相比，这种缩放方法具有许多优点：（i）CG参数直接与FG模型的参数相关（无需对独特的CG模型进行参数化）；（ii）对于具有相似s值的CG变体，预计几乎能实现理想混合（在s值相同的极限情况下实现理想混合）；（iii）应保留溶剂弛豫时间尺度（不存在粗粒度典型的动力学加速）；（iv）粒度级别N（由一个CG分子表示的FG分子数量）可以任意选择（特别是，N = s不一定是整数）；以及（v）在自适应分辨率方案中，该级别可以作为位置的函数连续变化（无需捆绑机制），并且这种变化在每个分子的粒子数恒定的情况下发生（缓冲层中不会出现分数自由度）。通过构建，AdSoS方案最小化了自适应分辨率系统不同区域之间的热力学不匹配，从而导致几乎均匀的缩放溶剂密度sρ。边界层内部和表面的残余密度伪影可以通过在初步纯溶剂模拟中构建的基于网格的偏置势轻松校正。本文介绍了AdSoS方案，并提供了其在平板几何结构中具有 Lennard-Jones 加库仑相互作用的纯原子液体（无溶质）的初步应用。
