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Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields

机译:三种糖力场对纤维素Iβ模拟的比较

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Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose Iβ microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose Iβ crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.
机译:由于对可再生能源应用的兴趣日益增加,纤维素的分子动力学模拟近来变得越来越普遍,并且存在许多可应用于纤维素的原子力和粗粒度力场。然而,迄今为止,尚未对该重要系统进行碳水化合物力场之间的系统比较。为此,我们提出了在室温下水合的36链纤维素Iβ微纤维的分子动力学模拟研究,具有三个碳水化合物力场(CHARMM35,GLYCAM06和Gromos 45a4),直至近微秒的时间尺度。我们的结果表明,在所测试的条件下,这些模拟的微纤维中的每一个都与纤维素Iβ晶体结构发生不同程度的偏离。 CHARMM35和GLYCAM06力场最终产生的结构类似于在500 K下观察到的结构,具有相同的力场,这与实验观察到的纤维素I的高温行为一致。第三力场Gromos 45a4产生的行为明显不同从实验,其他两个力场以及先前报告的使用该力场进行的仿真中,使用更短的仿真时间和受约束的周期性边界条件。对于GLYCAM06力场,初始氢键构象和静电定标因子的选择会显着影响结构的发散率。我们的结果表明,感兴趣的属性收敛的时间尺度截然不同,这在设计计算研究和与实验数据进行比较中很重要。这项研究强调,需要进一步的实验和理论研究来理解植物纤维素典型的小直径纤维素微纤维的结构。

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