Molecular dynamics: some recent developments in classical and quantum mechanical simulation of minerals

1995 ◽  
Vol 59 (397) ◽  
pp. 597-605 ◽  
Author(s):  
Lidunka Vočadlo ◽  
Atul Patel ◽  
Geoffrey D. Price
Keyword(s):  
Molecular Dynamics ◽  
Finite Temperature ◽  
High Pressures ◽  
Current Status ◽  
Quantum Mechanical ◽  
Empirical Potentials ◽  
Deep Interior ◽  
Recent Developments ◽  
High Pressures And Temperatures ◽  
Dynamics Simulations

AbstractWe review some of the most recent developments in classical and quantum mechanical molecular dynamics simulations, in particular as applied to Earth-forming phases at conditions prevalent in the Earth's deep interior. We pay special attention to the modelling of high pressures and temperatures, elucidating the problems associated with both the classical and quantum approaches in view of the empirical potentials required for the former, and the limitations of finite temperature calculations for the latter. We show the current status of such calculations for major phases such as MgSiO3 perovskite.

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations

2014 ◽  
Vol 10 (8) ◽  
pp. 3190-3199 ◽  
Author(s):  
David Semrouni ◽  
Ashwani Sharma ◽  
Jean-Pierre Dognon ◽  
Gilles Ohanessian ◽  
Carine Clavaguéra
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Finite Temperature ◽  
Dynamics Simulations

Molecular Dynamics Simulations on Melting of Aluminum

2013 ◽  
Vol 423-426 ◽  
pp. 935-938 ◽  
Author(s):  
Ji Feng Li ◽  
Xiao Ping Zhao ◽  
Jian Liu
Keyword(s):  
Molecular Dynamics ◽  
Melting Point ◽  
Molecular Dynamics Simulations ◽  
High Pressures ◽  
Ambient Pressure ◽  
Initial Porosity ◽  
Equilibrium Melting Point ◽  
Porosity Effect ◽  
Dynamics Simulations ◽  
Experimental Melting Point

Molecular dynamics simulations were performed to calculate the melting points of perfect crystalline aluminum to high pressures. Under ambientpressure, there exhibits about 20% superheating before melting compared to the experimental melting point. Under high pressures, thecalculated melting temperature increases with the pressure but at a decreasing rate, which agrees well with the Simon's melting equation. Porosity effect was also studied for aluminum crystals with various initial porosity at ambient pressure, which shows that the equilibrium melting point decreases with the initial porosity as experiments expect.

scholarly journals Systematic Finite-Temperature Reduction of Crystal Energy Landscapes.

2020 ◽  
Author(s):  
Nicholas Francia ◽  
Louise S. Price ◽  
Jonas Nyman ◽  
Sarah (Sally) Price ◽  
Matteo Salvalaglio
Keyword(s):  
Molecular Dynamics ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Lattice Energy ◽  
Biased Sampling ◽  
Energy Landscapes ◽  
Polymorphic Transformations ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
The Impact

<p>Crystal structure prediction methods are prone to overestimate the number of potential polymorphs of organic molecules. In this work, we aim to reduce the overprediction by systematically applying molecular dynamics simulations and biased sampling methods to cluster subsets of structures that can easily interconvert at finite temperature and pressure. Following this approach, we rationally reduce the number of predicted putative polymorphs in CSP-generated crystal energy landscapes. This uses an unsupervised clustering approach to analyze independent finite-temperature molecular dynamics trajectories and hence identify a representative structure of each cluster of distinct lattice energy minima that are effectively equivalent at finite temperature and pressure. Biased simulations are used to reduce the impact of limited sampling time and to estimate the work associated with polymorphic transformations. We demonstrate the proposed systematic approach by studying the polymorphs of urea and succinic acid, reducing an initial set of over 100 energetically plausible CSP structures to 12 and 27 respectively, including the experimentally known polymorphs. The simulations also indicate the types of disorder and stacking errors that may occur in real structures.<br></p>

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