scholarly journals Superscalability of the random batch Ewald method

2021 ◽  
Author(s):  
Jiuyang Liang ◽  
Pan Tan ◽  
Yue Zhao ◽  
Lei Li ◽  
Shi Jin ◽  
...  
Keyword(s):  
Ewald Method

Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Kazushi Fujimoto ◽  
Tetsuro Nagai ◽  
Tsuyoshi Yamaguchi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mass Velocity ◽  
Center Of Mass ◽  
Heterogeneous Systems ◽  
Diffusion Constant ◽  
Dynamics Simulation ◽  
Coulombic Interaction ◽  
Ewald Method ◽  
Theoretical Predictions

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

scholarly journals A Random Batch Ewald Method for Charged Particles in the Isothermal-Isobaric Ensemble

2021 ◽  
Author(s):  
Jiuyang Liang ◽  
Pan Tan ◽  
Liang Hong ◽  
Shi Jin ◽  
Zhenli Xu ◽  
...  
Keyword(s):  
Charged Particles ◽  
Ewald Method

High throughput identification of Li ion diffusion pathways in typical solid state electrolytes and electrode materials by BV-Ewald method

2019 ◽  
Vol 7 (3) ◽  
pp. 1300-1306 ◽  
Author(s):  
Dajun Chen ◽  
Jianshu Jie ◽  
Mouyi Weng ◽  
Shucheng Li ◽  
Dong Chen ◽  
...  
Keyword(s):  
Solid State ◽  
High Throughput ◽  
Electrode Materials ◽  
Ion Diffusion ◽  
Ewald Method ◽  
Li Ion ◽  
Solid State Electrolytes

A new BV-Ewald method was developed to calculate Li-ion diffusion pathways more quickly and correctly.

scholarly journals Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility

2009 ◽  
Vol 5 (9) ◽  
pp. 2322-2338 ◽  
Author(s):  
David S. Cerutti ◽  
Robert E. Duke ◽  
Thomas A. Darden ◽  
Terry P. Lybrand
Keyword(s):  
Particle Mesh Ewald ◽  
Ewald Method
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