论文标题
通过明显溶剂分子模拟预测溶液散射模式
Predicting solution scattering patterns with explicit-solvent molecular simulations
论文作者
论文摘要
小角度X射线或中子散射（SAXS/SANS/SAS）广泛用于获取有关溶液中生物分子或软物质复合物的结构信息。推导散射信号的分子解释需要从给定的原子结构模型预测SAS模式的方法。这样的SAS预测是非平凡的，因为模式受溶质的水合，排除的溶剂和热波动的影响。许多计算有效的方法使用简化的，隐式模型对水合层使用并排除溶剂，从而导致一些不确定性和需要与实验数据拟合的免费参数。 SAS基于明显溶剂分子动力学（MD）模拟以增加计算成本的价格克服了此类限制。为了合理化对明确溶剂方法的需求，我们首先回顾了隐式 - 溶剂方法的近似值。接下来，我们描述可通过WAXSIS Web服务器易于访问的显式溶剂SAS预测背后的理论。我们介绍了从给定的分子动力学轨迹计算SAS模式的工作流，并通过修改版本的Gromacs Simulations软件，即gromacs-swaxs可以免费获得，从而实现了WAXSIS方法。讨论了运行常规明确溶剂SAS预测的实际考虑。
Small-angle X-ray or neutron scattering (SAXS/SANS/SAS) is widely used to obtain structural information on biomolecules or soft-matter complexes in solution. Deriving a molecular interpretation of the scattering signals requires methods for predicting SAS patterns from a given atomistic structural model. Such SAS predictions are non-trivial because the patterns are influenced by the hydration layer of the solute, the excluded solvent, and by thermal fluctuations. Many computationally efficient methods use simplified, implicit models for the hydration layer and excluded solvent, leading to some uncertainties and to free parameters that require fitting against experimental data. SAS predictions based on explicit-solvent molecular dynamics (MD) simulations overcome such limitations at the price of an increased computational cost. To rationalize the need for explicit-solvent methods, we first review the approximations underlying implicit-solvent methods. Next, we describe the theory behind explicit-solvent SAS predictions that are easily accessible via the WAXSiS web server. We present the workflow for computing SAS pattern from a given molecular dynamics trajectory with a freely available via a modified version of the GROMACS simulations software, coined GROMACS-SWAXS, which implements the WAXSiS method. Practical considerations for running routine explicit-solvent SAS predictions are discussed.
