Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation

2018 ◽  
Vol 122 (9) ◽  
pp. 2495-2503 ◽  
Author(s):  
Kota Kasahara ◽  
Shun Sakuraba ◽  
Ikuo Fukuda
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Molecular Dynamics Simulations ◽  
Periodic Boundary ◽  
Peptide Conformation ◽  
Periodic Boundary Conditions ◽  
Enhanced Sampling ◽  
Dynamics Simulations

Computer-Generated Structural Models for a-Si:H

1988 ◽  
Vol 141 ◽  
Author(s):  
Laurent J. Lewis ◽  
Normand Mousseau ◽  
FranÇois Drolet
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Amorphous Silicon ◽  
Periodic Boundary ◽  
Hydrogenated Amorphous Silicon ◽  
Structural Models ◽  
Periodic Boundary Conditions ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous ◽  
Good Agreement

AbstractA new algorithm for generating fully-coordinated hydrogenated amorphous silicon models with periodic boundary conditions is presented. The hydrogen is incorporated into an a-Si matrix by a bond-switching process similar to that proposed by Wooten, Winer, and Weaire, making sure that four-fold coordination is preserved and that no rings with less than 5 members are created. After each addition of hydrogen, the structure is fully relaxed. The models so obtained, to be used as input to molecular dynamics simulations, are found to be in good agreement with experiment. A model with 12 at.% H is discussed in detail.

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