發展粗粒化振盪團簇模型於分子動力學模擬

The Coarse Grained Oscillating Blob Model for Molecular Dynamics Simulations

沈伯里(Boris Sandor)

指導教授 ： 趙聖德

國立臺灣大學/工學院/應用力學研究所/碩士(2020年)

https://doi.org/10.6342/NTU202004160

摘要

本文提出了一種新的用於分子動力學模擬的粗粒化模型。它在現有模型的基礎上，通過將小振動納入配方中，而不是將模擬分子視為剛性分子。正式推導了具有定義的幾何形狀和振動的兩個分子之間的勢能和力方程，並將其與以前的模型進行了對比。由於其對稱性和簡單的振盪模式，巴克敏斯特富勒烯被用於研究新模型的準確性。通過用參數的多項式函數近似由振動引起的變化，可以實現粗粒度電勢與完整原子電勢曲線的擬合。新方法可以對振動進行精確建模，並通過完整的原子模擬和其他粗粒度模型進行了驗證。還探討了系統動力學的溫度和振盪依賴性。

關鍵字

分子動力學 ； 粗粒度潛力 ； 震盪 ； 富勒烯

並列摘要

This thesis presents the development of a new coarse-grained model for molecular dynamics simulations. It builds on an existing model by incorporating small oscillations into the formulation rather than treating the simulated molecules as rigid. The equations for the potential and force between two molecules with a defined geometry and oscillation are formally derived and contrasted to the previous model. Due to its symmetry and simple oscillation modes Buckminsterfullerene is used to study the accuracy of the new model. The fitting of the coarse grained potential to the full atomistic potential curves is achieved by approximating the changes due to the oscillations with polynomial functions of the parameters. The new method accurately models the oscillations which is verified by full atomistic simulations and other coarse grained models. The temperature and oscillation dependence of the dynamics of the system is explored as well.

並列關鍵字

Molecular Dynamics ； Coarse-grained potential ； Oscillations ； Fullerene

參考文獻

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