# Method of information entropy for convergence assessment of molecular dynamics simulations

@article{Talaat2020MethodOI, title={Method of information entropy for convergence assessment of molecular dynamics simulations}, author={Khaled Talaat and Benjamin Cowen and Osman Anderoglu}, journal={Journal of Applied Physics}, year={2020}, volume={128}, pages={135102} }

The lack of a reliable method to evaluate the convergence of molecular dynamics simulations has contributed to discrepancies in different areas of molecular dynamics. In the present work, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon information entropy formalism is used to monitor the convergence of the atom motion to a steady state in a continuous spatial domain and is also used to assess the stationarity of calculated…

## References

SHOWING 1-10 OF 43 REFERENCES

Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?

- BiologyJ. Comput. Biol.
- 2011

It is concluded that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot, because the decisions are severely biased by different parameters.

Equivalence of the equilibrium and the nonequilibrium molecular dynamics methods for thermal conductivity calculations: From bulk to nanowire silicon

- Physics
- 2018

© 2018 American Physical Society. Molecular dynamics (MD) simulations play an important role in studying heat transport in complex materials. The lattice thermal conductivity can be computed either…

How good is damped molecular dynamics as a method to simulate radiation damage in metals

- Physics
- 2009

Classical molecular dynamics (MD) is a frequently used technique in the study of radiation damage cascades because it provides information on very small time and length scales inaccessible to…

Towards more accurate molecular dynamics calculation of thermal conductivity: Case study of GaN bulk crystals

- Engineering
- 2009

Significant differences exist among literature for thermal conductivity of various systems computed using molecular dynamics simulation. In some cases, unphysical results, for example, negative…

Length dependence of thermal conductivity by approach-to-equilibrium molecular dynamics

- Physics
- 2016

The length dependence of thermal conductivity over more than two orders of magnitude has been systematically studied for a range of materials, interatomic potentials, and temperatures using the…

Comparison of molecular dynamics methods and interatomic potentials for calculating the thermal conductivity of silicon.

- PhysicsThe Journal of chemical physics
- 2012

Green-Kubo and direct methods for calculating thermal conductivity κ are compared and it is argued that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si.

Non-equilibrium molecular dynamics calculation of heat conduction in liquid and through liquid-gas interface

- Physics
- 1994

This paper presents a new algorithm for non-equilibrium molecular dynamics, where a temperature gradient is established in a system with periodic boundary conditions. At each time step in the…

A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity

- Physics
- 1997

A nonequilibrium molecular dynamics method for calculating the thermal conductivity is presented. It reverses the usual cause and effect picture. The “effect,” the heat flux, is imposed on the system…

Size effects in molecular dynamics thermal conductivity predictions

- Physics
- 2010

We predict the bulk thermal conductivity of Lennard-Jones argon and Stillinger-Weber silicon using the Green-Kubo GK and direct methods in classical molecular dynamics simulations. While…