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Materials 2013, 6(3), 870-885; doi:10.3390/ma6030870
Article

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

1
, 2
 and 2,3,*
Received: 17 December 2012; in revised form: 22 February 2013 / Accepted: 4 March 2013 / Published: 6 March 2013
Download PDF [1867 KB, uploaded 6 March 2013]
Abstract: 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’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.
Keywords: elongation method; molecular dynamics; helix forming; hydrogen bond elongation method; molecular dynamics; helix forming; hydrogen bond
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Xie, P.; Orimoto, Y.; Aoki, Y. An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method. Materials 2013, 6, 870-885.

AMA Style

Xie P, Orimoto Y, Aoki Y. An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method. Materials. 2013; 6(3):870-885.

Chicago/Turabian Style

Xie, Peng; Orimoto, Yuuichi; Aoki, Yuriko. 2013. "An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method." Materials 6, no. 3: 870-885.


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