Fine-tuning property domain weighting factors and the objective function in force-field parameter optimization

IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS
Robin Strickstrock , Alexander Hagg , Marco Hülsmann , Karl N. Kirschner , Dirk Reith
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引用次数: 0

Abstract

Force field (FF) based molecular modeling is an often used method to investigate and study structural and dynamic properties of (bio-)chemical substances and systems. When such a system is modeled or refined, the force-field parameters need to be adjusted. This force-field parameter optimization can be a tedious task and is always a trade-off in terms of errors regarding the targeted properties. To better control the balance of various properties’ errors, in this study we introduce weighting factors for the optimization objectives. Different weighting strategies are compared to fine-tune the balance between bulk-phase density and relative conformational energies (RCE), using n-octane as a representative system. Additionally, a non-linear projection of the individual property-specific parts of the optimized loss function is deployed to further improve the balance between them. The results show that the combined error for the reproduction of the properties targeted in this optimization is reduced. Furthermore, the transferability of the force field parameters (FFParams) to chemically similar systems is increased. One interesting outcome is a large variety in the resulting optimized FFParams and corresponding errors, suggesting that the optimization landscape is multi-modal and very dependent on the weighting factor setup. We conclude that adjusting the weighting factors can be a very important feature to lower the overall error in the FF optimization procedure, giving researchers the possibility to fine-tune their FFs.

Abstract Image

力场参数优化中的微调特性域加权因子和目标函数
基于力场(FF)的分子建模是研究生物化学物质和系统的结构和动力学特性的常用方法。当对这样的系统进行建模或细化时,需要对力场参数进行调整。这种力场参数优化可能是一项繁琐的任务,并且总是在目标属性的错误方面进行权衡。为了更好地控制各种性能误差的平衡,本文在优化目标中引入了权重因子。以正辛烷为代表体系,比较了不同的加权策略来微调体相密度和相对构象能(RCE)之间的平衡。此外,优化损失函数的各个属性特定部分的非线性投影被部署,以进一步改善它们之间的平衡。结果表明,该优化方法减小了目标属性再现的综合误差。此外,力场参数(FFParams)在化学相似体系中的可转移性也得到了提高。一个有趣的结果是,优化后的FFParams和相应的误差有很大的差异,这表明优化是多模态的,并且非常依赖于权重因子的设置。我们得出结论,调整权重因子可以是降低FF优化过程中整体误差的一个非常重要的特征,使研究人员有可能微调他们的FF。
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来源期刊
Journal of molecular graphics & modelling
Journal of molecular graphics & modelling 生物-计算机:跨学科应用
CiteScore
5.50
自引率
6.90%
发文量
216
审稿时长
35 days
期刊介绍: The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design. As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.
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