scholarly journals Application of classical simulations for the computation of vibrational properties of free molecules

2016 ◽  
Vol 18 (40) ◽  
pp. 28325-28338 ◽  
Author(s):  
Denis S. Tikhonov ◽  
Dmitry I. Sharapa ◽  
Jan Schwabedissen ◽  
Vladimir V. Rybkin
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Vibrational Properties ◽  
Vibrational Motion ◽  
Classical Molecular Dynamics ◽  
Free Molecules

In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling of the intramolecular vibrational motion.

A method for analyzing nanomechanical deformation of nanocrystalline Ni at higher timesteps than is possible in classical molecular dynamics

2006 ◽  
Vol 978 ◽  
Author(s):  
Vikas Tomar
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Strain Rate ◽  
Defect Formation ◽  
Interatomic Potential ◽  
Md Simulations ◽  
Classical Molecular Dynamics ◽  
Rate Dependent ◽  
Nanocrystalline Structures ◽  
Defect Nucleation

AbstractA majority of computational mechanical analyses of nanocrystalline materials have been carried out using classical molecular dynamics (MD). Due to the fundamental reason that the MD simulations must resolve atomic level vibrations, they cannot be carried out at the timescale of the order of microseconds. Additionally, MD simulations have to be carried out at very high loading rates (∼108 s−1) rarely observed in experiments. In this investigation a modified Hybrid Monte Carlo (HMC) method that can be used to analyze time-dependent (strain rate dependent) atomistic mechanical deformation of nanocrystalline structures at higher timescales than currently possible using MD is established. In this method there is no restriction on the size of MD timestep except that it must be such that to ensure a reasonable acceptance rate between consecutive Monte-Carlo (MC) time-steps. For the purpose of comparison HMC analyses of a nanocrystalline Ni sample at a strain rate of 109 s−1 with three different timesteps, viz. 2 fs, 4fs, and 8 fs, are compared with the analyses based on MD simulations at the same strain rate and a MD timestep of 2 fs. MD simulations of nanocrystalline Ni reproduce the defect nucleation and propagation results as well as strength values reported in the literature. In addition, HMC with timestep of 8 fs correctly reproduces defect formation and stress-strain response observed in the case of MD simulations with permissible timestep of 2 fs (for the interatomic potential used 2 fs is the highest MD timestep). Simulation time analyses show that by using HMC a saving of the order of 4 can be achieved bringing the atomistic analyses closer to the continuum timescales.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Numerical Methods for the Kinetic Theory of Fluids

2018 ◽  
Author(s):  
Sauro Succi
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Numerical Methods ◽  
Kinetic Theory ◽  
Computational Efficiency ◽  
Lattice Boltzmann ◽  
Direct Simulation Monte Carlo ◽  
Particle Methods ◽  
Direct Simulation ◽  
Simulation Monte Carlo

This chapter provides a bird’s eye view of the main numerical particle methods used in the kinetic theory of fluids, the main purpose being of locating Lattice Boltzmann in the broader context of computational kinetic theory. The leading numerical methods for dense and rarified fluids are Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC), respectively. These methods date of the mid 50s and 60s, respectively, and, ever since, they have undergone a series of impressive developments and refinements which have turned them in major tools of investigation, discovery and design. However, they are both very demanding on computational grounds, which motivates a ceaseless demand for new and improved variants aimed at enhancing their computational efficiency without losing physical fidelity and vice versa, enhance their physical fidelity without compromising computational viability.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

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