Xie Peng, Orimoto Yuuichi, Aoki Yuriko
Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan.
Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan.
Materials (Basel). 2013 Mar 6;6(3):870-885. doi: 10.3390/ma6030870.
A new local molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atom's nucleus in the active region are calculated by the ELG method while the equations of the nucleus's motion are solved by the GPC algorithm. In this work, the first application of this ELG-MD method is described to investigate the stable conformation of polyglycine with surrounding water molecules. The water effects on the structure of polyglycine are examined. The ELG-MD simulations show that the formation of the polyglycine helix is strongly induced by the hydrogen bonds observed in two types of H-bond rings.
提出了一种新的局部分子动力学方法，即伸长分子动力学（ELG-MD），用于对非周期性聚合物系统进行高效模拟。ELG-MD将伸长方法（ELG）与分子动力学模拟的Gear预测校正（GPC）算法相结合。在该方法中，通过ELG方法计算作用于活性区域中原子核的局部梯度，同时通过GPC算法求解原子核的运动方程。在这项工作中，描述了这种ELG-MD方法的首次应用，以研究聚甘氨酸与周围水分子的稳定构象。研究了水对聚甘氨酸结构的影响。ELG-MD模拟表明，在两种类型的氢键环中观察到的氢键强烈诱导了聚甘氨酸螺旋的形成。
