Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses

2010 ◽  
Vol 78 (16) ◽  
pp. 3341-3352 ◽  
Author(s):  
Aqeel Ahmed ◽  
Saskia Villinger ◽  
Holger Gohlke
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Normal Mode ◽  
Large Scale ◽  
Coarse Grained ◽  
Essential Dynamics ◽  
Dynamics Simulations

scholarly journals Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics

2021 ◽  
Author(s):  
Mei Zheng ◽  
Andres Jaramillo-Botero ◽  
Xue-hai Ju ◽  
William A. Goddard
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Equation Of State ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Coarse Grained ◽  
Polyacrylamide Gels ◽  
Dynamics Simulations

Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.

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 Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

scholarly journals Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth

2016 ◽  
Vol 34 (4) ◽  
pp. 041509 ◽  
Author(s):  
Daniel Edström ◽  
Davide G. Sangiovanni ◽  
Lars Hultman ◽  
Ivan Petrov ◽  
J. E. Greene ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Epitaxial Film ◽  
Film Growth ◽  
Dynamics Simulations ◽  
Epitaxial Film Growth
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