scholarly journals Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins

2009 ◽  
Vol 30 (16) ◽  
pp. 2635-2644 ◽  
Author(s):  
Mehdi Bagheri Hamaneh ◽  
Matthias Buck
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Shell Model ◽  
Hydration Shell ◽  
Large Proteins ◽  
Dynamics Simulations

scholarly journals Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Dipole Moments ◽  
Hydration Shell ◽  
Minor Groove ◽  
Water Molecules ◽  
Negative Hydration ◽  
Dynamics Simulations ◽  
Dna Double Helix

The DNA double helix is a polyanionic macromolecule that is neutralized in water solutions by metal ions (counterions). The property of counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na+ counterions and negative hydration of K+ and Cs+ counterions incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on the region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions localized in the minor groove of the double helix (about 50 ps for Na+ and lower than 10 ps for K+ and Cs+). The estimated potentials of the mean force for the hydration shells of counterions show that the water molecules are constrained too strongly, and the effect of negative hydration for K+ and Cs+ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

scholarly journals Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

2020 ◽  
Vol 16 (3) ◽  
pp. 1866-1881 ◽  
Author(s):  
Victor Ovchinnikov ◽  
Simone Conti ◽  
Edmond Y. Lau ◽  
Felice C. Lightstone ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Shell Model ◽  
Solvation Shell ◽  
Quasi Equilibrium ◽  
Dynamics Simulations

Molecular dynamics simulations of hydration shell on montmorillonite (001) in water

2016 ◽  
Vol 48 (9) ◽  
pp. 976-980 ◽  
Author(s):  
Hao Yi ◽  
Xian Zhang ◽  
Yunliang Zhao ◽  
Lingyun Liu ◽  
Shaoxian Song
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydration Shell ◽  
Dynamics Simulations
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