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An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package
Journal of Cheminformatics ( IF 7.1 ) Pub Date : 2024-08-08 , DOI: 10.1186/s13321-024-00890-5
Felix Bänsch 1 , Mirco Daniel 1 , Harald Lanig 2 , Christoph Steinbeck 3 , Achim Zielesny 1
Affiliation  

An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. Scientific Contribution To our knowledge, there is currently no open computational pipeline for differential pair interaction energies at all. This work aims to contribute an (at least academically available, open) approach based on molecular force fields that provides a robust and efficient computational scheme for their automated calculation for small to medium-sized (organic) molecular dimers. The usefulness of the proposed new calculation scheme is demonstrated for the generation of mesoscopic particles with their mutual repulsive interactions.

中文翻译:


使用 Tinker 分子建模包自动计算差分对相互作用能量与分子力场



提出了使用 Tinker 分子建模包基于分子力场综合计算分子间相互作用能的自动化管道。从非优化的化学直观单体结构开始,该流程允许近似全局最小能量单体和二聚体、各种单体-单体距离的构型采样、通过分子动力学模拟估计配位数以及微分对相互作用能量的评估。后者用于导出耗散粒子动力学 (DPD) 的 Flory-Huggins 参数和各向同性粒子间斥力。使用密度泛函理论 (DFT) 计算和 DPD 模拟对非离子聚氧乙烯烷基醚表面活性剂 C10E4 与水的混合物分析力场 MM3、MMFF94、OPLS-AA 和 AMOEBA09 的计算结果,以证明该方法的有用性。科学贡献 据我们所知,目前根本没有针对差分对相互作用能量的开放计算管道。这项工作旨在贡献一种基于分子力场的(至少在学术上可用的、开放的)方法,为中小型(有机)分子二聚体的自动计算提供强大且高效的计算方案。所提出的新计算方案对于生成具有相互排斥相互作用的介观粒子而言是有用的。
更新日期:2024-08-09
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