System size dependence and time convergence in molecular dynamics simulations of monolayer films

1991 ◽  
Vol 95 (1) ◽  
pp. 540-543 ◽  
Author(s):  
Marvin Bishop ◽  
Julian H. R. Clarke
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
System Size ◽  
Monolayer Films ◽  
Dynamics Simulations

scholarly journals Thermal Properties of Yttrium Aluminum Garnett From Molecular Dynamics Simulations

2011 ◽  
Author(s):  
Majid S. al-Dosari ◽  
D. G. Walker
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Expansion ◽  
Thermal Properties ◽  
Specific Heat ◽  
Molecular Dynamics Simulations ◽  
Yttrium Aluminum Garnet ◽  
System Size ◽  
Yttrium Aluminum ◽  
Dynamics Simulations

Yttrium Aluminum Garnet (YAG, Y3Al5O12) and its varieties have applications in thermographic phosphors, lasing mediums, and thermal barriers. In this work, thermal properties of crystalline YAG where aluminum atoms are substituted with gallium atoms (Y3(Al1−xGax)5O12) are explored with molecular dynamics simulations. For YAG at 300K, the simulations gave values close to experimental values for constant-pressure specific heat, thermal expansion, and bulk thermal conductivity. For various values of x, the simulations predicted no change in thermal expansion, an increase in specific heat, and a decrease in thermal conductivity for x = 50%. Furthermore, the simulations predicted a decrease in thermal conductivity with decreasing system size.

Methane Hydrate Nucleation Rates from Molecular Dynamics Simulations: Effects of Aqueous Methane Concentration, Interfacial Curvature, and System Size

2011 ◽  
Vol 115 (43) ◽  
pp. 21241-21248 ◽  
Author(s):  
Matthew R. Walsh ◽  
Gregg T. Beckham ◽  
Carolyn A. Koh ◽  
E. Dendy Sloan ◽  
David T. Wu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Methane Hydrate ◽  
Methane Concentration ◽  
System Size ◽  
Dynamics Simulations

Molecular dynamics simulations of the diffusion of benzene sub-monolayer films on graphite basal plane surfaces

Carbon ◽  
2009 ◽  
Vol 47 (11) ◽  
pp. 2627-2639 ◽  
Author(s):  
Peter Fouquet ◽  
Mark R. Johnson ◽  
Holly Hedgeland ◽  
Andrew P. Jardine ◽  
John Ellis ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Basal Plane ◽  
Monolayer Films ◽  
Graphite Basal Plane ◽  
Dynamics Simulations

scholarly journals Comment on ‘Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’

2019 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L. de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

AbstractA recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed. Here, we express three main concerns about that study. In addition, we show that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

scholarly journals Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

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