scholarly journals Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Based ab Initio Molecular Dynamics

2019 ◽  
Vol 10 (14) ◽  
pp. 3877-3886 ◽  
Author(s):  
Jie Liu ◽  
Bhaskar Rana ◽  
Kuan-Yu Liu ◽  
John M. Herbert
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Variational Formulation ◽  
Ab Initio Molecular Dynamics ◽  
Many Body ◽  
Energy Gradient ◽  
Self Consistent

scholarly journals Static and Dynamic Statistical Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature With Path Integral Simulations at Ambient Temperature

2022 ◽  
Author(s):  
Chenghan Li ◽  
Francesco Paesani ◽  
Gregory A. Voth
Keyword(s):  
Molecular Dynamics ◽  
Elevated Temperature ◽  
Ambient Temperature ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Many Body ◽  
Statistical Correlations ◽  
Higher Temperature ◽  
The Many

It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the over-structuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. We find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature.

scholarly journals Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3120
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Combustion Process ◽  
Computational Cost ◽  
Reaction Network ◽  
Methane Combustion ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Many Body ◽  
Experimental Findings

We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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