Fast and slow dynamics and the local structure of liquid and supercooled water next to a hydrophobic amino acid

2016 ◽  
Vol 18 (39) ◽  
pp. 27639-27647 ◽  
Author(s):  
H. F. M. C. Martiniano ◽  
N. Galamba
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Freezing Point ◽  
Supercooled Water ◽  
Slow Dynamics ◽  
Hydrophobic Amino Acid ◽  
Dynamics Simulations ◽  
Structure Of Liquid

We study, through molecular dynamics simulations, the structure and orientational dynamics of water next to a blocked hydrophobic amino acid, valine (Val), above and below the freezing point of water.

scholarly journals The Anomalies and Local Structure of Liquid Water from Many-Body Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Thomas E. Gartner III ◽  
Kelly M. Hunter ◽  
Eleftherios Lambros ◽  
Alessandro Caruso ◽  
Marc Riera ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Liquid Water ◽  
Local Structure ◽  
Ambient Pressure ◽  
Liquid Density ◽  
Many Body ◽  
The Many ◽  
Dynamics Simulations ◽  
Structure Of Liquid

For the last 50 years, researchers have sought molecular models that can accurately reproduce water’s microscopic structure and thermophysical properties across broad ranges of its complex phase diagram. Herein, molecular dynamics simulations with the many-body MB-pol model are performed to monitor the thermodynamic response functions and local structure of liquid water from the boiling point down to deeply supercooled temperatures at ambient pressure. The isothermal compressibility and isobaric heat capacity show maxima at ~223 K, in excellent agreement with recent experiments, and the liquid density exhibits a minimum at ~208 K. Furthermore, a local tetrahedral arrangement, where each water molecule accepts and donates two hydrogen bonds, is the most probable hydrogen-bonding topology at all temperatures. This work suggests that MB-pol may provide predictive capability for studies of liquid water’s physical properties across broad ranges of thermodynamic states.

Local structure of liquid CaAl2O4 from ab initio molecular dynamics simulations

2008 ◽  
Vol 354 (47-51) ◽  
pp. 5337-5339 ◽  
Author(s):  
V. Cristiglio ◽  
L. Hennet ◽  
G.J. Cuello ◽  
I. Pozdnyakova ◽  
M.R. Johnson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations ◽  
Structure Of Liquid

scholarly journals New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations
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