Indirubin is a natural-product-based medication, derived from the traditional Chinese medicine dangguilonghui pill (DLP), which is composed of 11 Chinese herbs and is used clinically to treat chronic myeloid leukemia (Gaboriaud-Kolar, Vougogiannopoulou, & Skaltsounis, 2015). After further research, it has been found that the main chemically active ingredient of DLP is indigo naturalis (qing-dai; Tokuyasu et al., 2018). Although the indigo content in qing-dai is high, the main active ingredient for the treatment of leukemia is indirubin, the isomer of indigo (Gaitanis, Magiatis,
Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about diatomic molecular system and 2 triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite element method is also a reliable method to simulate long-time classical trajectory of molecular systems.
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