Wielding the power of interactive molecular simulations

2021 ◽  
Author(s):  
André Lanrezac ◽  
Nicolas Férey ◽  
Marc Baaden
Keyword(s):  
Molecular Simulations

CALIBRATION AND RANKING OF COARSE-GRAINED MODELS IN MOLECULAR SIMULATIONS USING BAYESIAN FORMALISM

2017 ◽  
Vol 7 (2) ◽  
pp. 99-115 ◽  
Author(s):  
Hadi Meidani ◽  
Justin B. Hooper ◽  
Dmitry Bedrov ◽  
Robert M. Kirby
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulations

2019 ◽  
Author(s):  
Riccardo Spezia ◽  
Hichem Dammak
Keyword(s):  
Degrees Of Freedom ◽  
Molecular Simulations ◽  
Zero Point ◽  
Thermal Bath ◽  
Unimolecular Dissociation ◽  
Point Energy ◽  
Rotational Degrees Of Freedom ◽  
The Difference ◽  
Nuclear Effects

<div> <div> <div> <p>In the present work we have investigated the possibility of using the Quantum Thermal Bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is aimed in introducing quantum nuclear effects with a com- putational time which is basically the same as in newtonian simulations. At this end we have considered the model fragmentation of CH4 for which an analytical function is present in the literature. Moreover, based on the same model a microcanonical algorithm which monitor zero-point energy of products, and eventually modifies tra- jectories, was recently proposed. We have thus compared classical and quantum rate constant with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study unimolecular fragmentation of much complex systems with molecular simulations. The role of QTB thermostat on rotational degrees of freedom is also analyzed and discussed. </p> </div> </div> </div>

Hydrodynamic slippage of water at surfaces

2017 ◽  
Author(s):  
E. Charlaix ◽  
L. Bocquet
Keyword(s):  
Boundary Condition ◽  
Molecular Mechanisms ◽  
Slip Length ◽  
Molecular Simulations ◽  
Short Review ◽  
Solid Surfaces ◽  
Experimental Investigations

The boundary condition (B.C.) for hydrodynamic flows at solid surfaces is usually assumed to be that of no slip. However a number of molecular simulations and experimental investigations over the last two decades have demonstrated violations of the no-slip B.C., leading to hydrodynamic slippage at solid surfaces. In this short review, we explore the molecular mechanisms leading to hydrodynamic slippage of water at various surfaces and discuss experimental investigations allowing us to measure the so-called slip length

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