Structure and Dynamics of Metal Ions in Solution:  QM/MM Molecular Dynamics Simulations of Mn2+and V2+

2003 ◽  
Vol 125 (6) ◽  
pp. 1618-1624 ◽  
Author(s):  
Christian F. Schwenk ◽  
Hannes H. Loeffler ◽  
Bernd M. Rode
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Structure And Dynamics ◽  
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>

scholarly journals Membrane potential and dynamics in a ternary lipid mixture: insights from molecular dynamics simulations

2018 ◽  
Vol 20 (23) ◽  
pp. 15841-15851 ◽  
Author(s):  
Xubo Lin ◽  
Vinay Nair ◽  
Yong Zhou ◽  
Alemayehu A. Gorfe
Keyword(s):  
Molecular Dynamics ◽  
Membrane Potential ◽  
Molecular Dynamics Simulations ◽  
Transmembrane Potential ◽  
Lipid Mixture ◽  
Structure And Dynamics ◽  
Head Groups ◽  
Acyl Chains ◽  
Dynamics Simulations

Transmembrane potential modulates the structure and dynamics of lipid head-groups and acyl chains.

Structure and dynamics of gold nanoparticles decorated with chitosan–gentamicin conjugates: ReaxFF molecular dynamics simulations to disclose drug delivery

2019 ◽  
Vol 21 (24) ◽  
pp. 13099-13108 ◽  
Author(s):  
Susanna Monti ◽  
Jiya Jose ◽  
Athira Sahajan ◽  
Nandakumar Kalarikkal ◽  
Sabu Thomas
Keyword(s):  
Drug Delivery ◽  
Molecular Dynamics ◽  
Gold Nanoparticles ◽  
Molecular Dynamics Simulations ◽  
Atomic Scale ◽  
Functionalized Gold Nanoparticles ◽  
Structure And Dynamics ◽  
Antibiotic Drug ◽  
Dynamics Simulations

Functionalized gold nanoparticles for antibiotic drug delivery: from the nanoscale to the atomic scale.

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