Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations

2009 ◽  
Vol 113 (30) ◽  
pp. 10255-10260 ◽  
Author(s):  
Jens Carlsson ◽  
Johan Åqvist
Keyword(s):  
Molecular Dynamics ◽  
Alkali Metal ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Alkali Metal Ions ◽  
Dynamics Simulations

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

Stability and Migration of Metal Ions in G4-Wires by Molecular Dynamics Simulations

2006 ◽  
Vol 110 (51) ◽  
pp. 26337-26348 ◽  
Author(s):  
Manuela Cavallari ◽  
Arrigo Calzolari ◽  
Anna Garbesi ◽  
Rosa Di Felice
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
And Migration ◽  
Dynamics Simulations

Metal ions affect the formation and stability of amyloid β aggregates at multiple length scales

2018 ◽  
Vol 20 (13) ◽  
pp. 8951-8961 ◽  
Author(s):  
Myeongsang Lee ◽  
Jae In Kim ◽  
Sungsoo Na ◽  
Kilho Eom
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Neurodegenerative Disease ◽  
Molecular Dynamics Simulations ◽  
Metal Ion ◽  
Amyloid Β ◽  
Length Scales ◽  
Multiple Length Scales ◽  
Dynamics Simulations

The effect of metal ion on the formation of amyloid β (Aβ) aggregates, which are a hallmark for neurodegenerative disease, was studied based on full atomistic molecular dynamics simulations.

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