scholarly journals Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations

2019 ◽  
Vol 123 (24) ◽  
pp. 5099-5106 ◽  
Author(s):  
Martin Vögele ◽  
Jürgen Köfinger ◽  
Gerhard Hummer
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Molecular Dynamics Simulations ◽  
Diffusion Coefficients ◽  
Rotational Diffusion ◽  
Finite Size ◽  
Rotational Diffusion Coefficients ◽  
Dynamics Simulations

Diffusion coefficients of penetrant gases in polyisobutylene can be calculated correctly by molecular-dynamics simulations

1992 ◽  
Vol 25 (24) ◽  
pp. 6722-6724 ◽  
Author(s):  
Florian Mueller-Plathe ◽  
Stephen C. Rogers ◽  
Wilfred F. Van Gunsteren
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Diffusion Coefficients ◽  
Dynamics Simulations

scholarly journals Self-Diffusion Coefficients of Methane/n-Hexane Mixtures at High Pressures: An Evaluation of the Finite-Size Effect and a Comparison of Force Fields

2019 ◽  
Author(s):  
Thiago José Pinheiro dos Santos ◽  
Charlles Abreu ◽  
Bruno Horta ◽  
Frederico W. Tavares
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
High Pressures ◽  
Force Fields ◽  
Transport Coefficients ◽  
Finite Size ◽  
Finite Size Effect ◽  
Self Diffusion ◽  
Analytical Correction ◽  
Dynamics Simulations

Mass transport coefficients play an important role in process design and in compositional grading of oil reservoirs. As experimental measurements of these properties can be costly and hazardous, Molecular Dynamics simulations emerge as an alternative approach. In this work, we used Molecular Dynamics to calculate the self-diffusion coefficients of methane/n-hexane mixtures at different conditions, in both liquid and supercritical phases. We evaluated how the finite box size and the choice of the force field affect the calculated properties at high pressures. Results show a strong dependency between self-diffusion and the simulation box size. The Yeh-Hummer analytical correction [J. Phys. Chem. B, 108, 15873 (2004)] can attenuate this effect, but sometimes makes the results depart from experimental data due to issues concerning the force fields. We have also found that different all-atom and united-atom models can produce biased results due to caging effects and to different dihedral configurations of the n-alkane.

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