In this work, we performed fully atomistic classical molecular dynamics simulations to characterize the structural and energetic interaction of peptide nanoribbons/nanofibers with different lengths. The nanostructures are formed by peptides used in the release of bioactive molecules and tissue regeneration, composed of lysine (K), serine (S) and leucine (L), in the following sequence K2(SL)6K2. The simulations were performed and analyzed in isobaric-isothermal (NPT) and isovolumetric-isothermal (NVT) ensembles. Our results evaluate how these nanostructures are stabilized by the hydrogen bonds (HB) between the peptides. In general, the average number of these HBs is between 5 and 6 HBs per peptide in the nanostructure, with a lifetime that can reach up to 2.2 ns and a cut-off energy of about 23 kJ/mol. All analyzes are considered in structures with lengths varying from 6 to 18 nm which represents a careful study of tape/fiber simulations.

中文翻译：

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使用分子动力学模拟对短和长肽纳米带/纳米纤维中的氢键进行统计和能量分析


在这项工作中，我们进行了全原子经典分子动力学模拟，以表征不同长度的肽纳米带/纳米纤维的结构和能量相互作用。纳米结构由用于生物活性分子释放和组织再生的肽形成，由赖氨酸 （K）、丝氨酸 （S） 和亮氨酸 （L） 组成，顺序如下 K2（SL）6K2。在等压-等温 （NPT） 和等体积-等温 （NVT） 集合中进行模拟和分析。我们的结果评估了肽之间的氢键 （HB） 如何稳定这些纳米结构。一般来说，这些 HB 的平均数量在纳米结构中每个肽 5 到 6 个 HB 之间，寿命可达 2.2 ns，截止能量约为 23 kJ/mol。所有分析均在长度从 6 到 18 nm 不等的结构中考虑，这代表了对胶带/纤维模拟的仔细研究。