An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method

作者：Xie Peng; Orimoto Yuuichi; Aoki Yuriko^*

来源：Materials, 2013, 6(3): 870-885.

DOI：10.3390/ma6030870

• elongation method
• molecular dynamics
• helix forming
• hydrogen bond

A new local ab initio 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%26apos;s nucleus in the active region are calculated by the ELG method while the equations of the nucleus%26apos;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.

• 出版日期2013-3