skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A novel energy conversion based method for velocity correction in molecular dynamics simulations

Abstract

Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

Authors:
 [1];  [2];  [1];  [1];  [3]
  1. School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China)
  2. (China)
  3. State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027 (China)
Publication Date:
OSTI Identifier:
22622291
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Computational Physics; Journal Volume: 336; Other Information: Copyright (c) 2017 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ATOMS; COMPUTERIZED SIMULATION; CORRECTIONS; ENERGY CONVERSION; EQUILIBRIUM; FLUIDS; INTERACTIONS; MOLECULAR DYNAMICS METHOD; MOLECULES; SOLIDS; VELOCITY

Citation Formats

Jin, Hanhui, Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027, Liu, Ningning, Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn, and Fan, Jianren. A novel energy conversion based method for velocity correction in molecular dynamics simulations. United States: N. p., 2017. Web. doi:10.1016/J.JCP.2017.02.028.
Jin, Hanhui, Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027, Liu, Ningning, Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn, & Fan, Jianren. A novel energy conversion based method for velocity correction in molecular dynamics simulations. United States. doi:10.1016/J.JCP.2017.02.028.
Jin, Hanhui, Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027, Liu, Ningning, Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn, and Fan, Jianren. Mon . "A novel energy conversion based method for velocity correction in molecular dynamics simulations". United States. doi:10.1016/J.JCP.2017.02.028.
@article{osti_22622291,
title = {A novel energy conversion based method for velocity correction in molecular dynamics simulations},
author = {Jin, Hanhui and Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027 and Liu, Ningning and Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn and Fan, Jianren},
abstractNote = {Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.},
doi = {10.1016/J.JCP.2017.02.028},
journal = {Journal of Computational Physics},
number = ,
volume = 336,
place = {United States},
year = {Mon May 01 00:00:00 EDT 2017},
month = {Mon May 01 00:00:00 EDT 2017}
}
  • The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method canmore » calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.« less
  • We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard–Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated undermore » three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.« less
  • Cited by 2
  • Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance themore » oxygen adsorption and to promote catalytic reactions.« less
  • Using molecular dynamics simulations, the melting points and liquid phase dynamic properties were studied for four alkyl-imidazolium-based ionic liquids, 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), 1-n-butyl-2,3-dimethylimidazolium hexafluorophosphate ([BMMIM][PF6]), 1-ethyl-3-methylimidazolium hexafluorophosphate ([EMIM][PF6]), and 1-ethyl-2,3-dimethylimidazolium hexafluorophosphate ([EMMIM][PF6]), respectively. Experimentally it has been observed that the substitution of a methyl group for a hydrogen at the C2 position of the cation ring leads to an increase in both the melting point and liquid phase viscosity, contrary to arguments that had been made regarding associations between the ions. The melting points of the four ionic liquids were accurately predicted using simulations, as were the trends in viscosity.more » The simulation results show that the origin of the effect is mainly entropic, although enthalpy also plays an important role.« less