A molecular dynamics method for simulations in the canonical ensemble

Nosé, Shūichi

doi:10.1080/00268970110089108

Cited by 1,068 publications

(1,003 citation statements)

References 17 publications

Supporting

Mentioning

991

Contrasting

Unclassified

Order By: Relevance

“…In the real physical process heat generated by viscous dissipation would be conducted through the wall so that the system can keep a constant temperature. Therefore, in MD simulation, there are several special methods must be adopted in the MDS to keep the constant temperature (Andersen 1980;Berendsen et al 1984;Nose 1984Nose , 2002Hoover 1985). A relaxing method (Buckingham 1938) was developed by coupling an external bath at a constant temperature to the system and modifying the velocities at each iteration through a differential feedback mechanism.…”

Section: Thermal Wall Models For Viscous Dissipation Effectmentioning

confidence: 99%

Molecular dynamics simulation of nanoscale liquid flows

2010

Microfluid Nanofluid

138

View full text Add to dashboard Cite

Molecular dynamics (MD) simulation is a powerful tool to investigate the nanoscale fluid flow. In this article, we review the methods and the applications of MD simulation in liquid flows in nanochannels. For pressuredriven flows, we focus on the fundamental research and the rationality of the model hypotheses. For electrokineticdriven flows and the thermal-driven flows, we concentrate on the principle of generating liquid motion. The slip boundary condition is one of the marked differences between the macro-and micro-scale flows and the nanoscale flows. In this article, we review the parameters controlling the degree of boundary slip and the new findings. MD simulation is based on the Newton's second law to simulate the particles' interactions and consists of several important processing methods, such as the thermal wall model, the cut-off radius, and the initial condition. Therefore, we also reviewed the recent improvement in these key methods to make the MD simulation more rational and efficient. Finally, we summarized the important discoveries in this research field and proposed some worthwhile future research directions.

show abstract

Section: Thermal Wall Models For Viscous Dissipation Effectmentioning

confidence: 99%

Molecular dynamics simulation of nanoscale liquid flows

2010

Microfluid Nanofluid

138

View full text Add to dashboard Cite

show abstract

“…The time step for this algorithm was set to t √ 1 /m 1 /σ 1 = 0.001. The time-correlation functions were calculated in the NV T ensemble using the Nosé-Hoover thermostat [30,31] with a thermal inertial parameter of 10 kJ · mol −1 · ps 2 , and the diffusion coefficients were then obtained by using Eqs. (5) and (6).…”

Section: Simulation Detailsmentioning

confidence: 99%

Self-Diffusion and Binary Maxwell–Stefan Diffusion Coefficients of Quadrupolar Real Fluids from Molecular Simulation

2005

View full text Add to dashboard Cite

Self-and binary Maxwell-Stefan diffusion coefficients were determined by equilibrium molecular dynamics simulations with the Green-Kubo method. This study covers selfdiffusion coefficients at liquid states for eight pure fluids, i.e. F 2 , N 2 , CO 2 , CS 2 , C 2 H 6 , C 2 H 4 , C 2 H 2 and SF 6 as well as Maxwell-Stefan diffusion coefficients for three binary mixtures N 2 +CO 2 , N 2 +C 2 H 6 and CO 2 +C 2 H 6 . The fluids were modeled by the two-center Lennard-Jones plus point-quadrupole pair potential, with parameters taken from previous work of our group which were determined solely on the basis of vapor-liquid equilibrium data. Self-diffusion coefficients are predicted with a statistical uncertainty less than 1% and they agree within 2% to 28% with the experimental data. The correction of the simulation data due to the finite size of the system increases the value of the self-diffusion coefficient typically by 10%. If this correction is considered, better agreement with the experimental data can be expected for most of the studied fluids. Maxwell-Stefan diffusion coefficients for three binary mixtures were also predicted, their statistical uncertainty is about 10%. These results were used to test three empirical equations to estimate Maxwell-

show abstract

“…The temperature was kept constant at 298 K by using a Nose´-Hoover thermostat [29,30] with a relaxation time of 2 ps. A Rahman-Parrinello barostat [31] (coupling time 5 ps with an isothermal compressibility of 4.5 × 10 −5 bar −1 ) were employed when constant pressure simulations were needed.…”

Section: Computational Detailsmentioning

confidence: 99%

A coarse-grained model for polylactide: glass transition temperature and conformational properties

Prasitnok

2016

J Polym Res

View full text Add to dashboard Cite

In this article, we present a coarse-grained (CG) model of poly(lactic acid) (PLA) developed by the iterative Boltzmann inversion (IBI) method. The coarse-grained potential was derived by matching the structural probability distribution functions to those of reference atomistic simulation. The resulting coarse-grained potential was found to be temperaturedependent when trying to reproduce the thermal expansion behavior of PLA. To satisfactory reproduce this behavior, the potential needs to be modified by a temperature factor of (T/T 0 ) 0.3 ; T 0 = 327 K is the temperature at which the potential has been derived. The glass transition temperature (T g ) as predicted by the modified CG potential compared favorably with those from experiment and atomistic simulation. Chain conformational properties were also evaluated in terms of a chain length (N)-radius of gyration (R g ) relation and the persistence length. The model we develop was also noted to provide a considerable speed-up of computer time compared to its atomistic counterpart.

show abstract

A molecular dynamics method for simulations in the canonical ensemble

Cited by 1,068 publications

References 17 publications

Molecular dynamics simulation of nanoscale liquid flows

Molecular dynamics simulation of nanoscale liquid flows

Self-Diffusion and Binary Maxwell–Stefan Diffusion Coefficients of Quadrupolar Real Fluids from Molecular Simulation

A coarse-grained model for polylactide: glass transition temperature and conformational properties

Contact Info

Product

Resources

About