Ewald summation and multiple time step methods for molecular dynamics simulation of biological molecules

2000 ◽  
Vol 530 (3) ◽  
pp. 237-243 ◽  
Author(s):  
Y. Komeiji
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Multiple Time ◽  
Ewald Summation ◽  
Time Step ◽  
Multiple Time Step

Investigation of Fractional Characteristic of Molecular Motion by Molecular Dynamics Simulation

2004 ◽  
Author(s):  
Chao Liu ◽  
Liming Wan ◽  
Xinming Zhang ◽  
Danling Zeng
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Vapor Phase ◽  
Molecular Motion ◽  
Mean Free Path ◽  
Dynamics Simulation ◽  
Fractional Dimension ◽  
Time Step ◽  
Vapor Interface ◽  
Liquid Vapor

Molecular dynamics simulation (MDS) is adopted to investigate the characteristic of fractional motion of molecules in liquid phase, vapor phase and liquid-vapor interface in the paper. Based on the theory of mean free path and Shannon sampling theorem, the way to determine a universal criterion of time step of simulation is presented. It is shown that there exists difference in the regular pattern of molecular motion in the state of liquid and vapor phase. The fractional features are different for different matter states. Under the condition of same temperature, the characteristic fractional number of molecular motion in liquid state is greater than one in vapor state. It is shown that the fractional dimension numbers in the X, Y and Z direction of the liquid-vapor interface are different. This proves that the liquid-vapor interface has anisotropic character.

Multiple time-step methods in molecular dynamics

1978 ◽  
Vol 35 (3) ◽  
pp. 639-648 ◽  
Author(s):  
W.B. Streett ◽  
D.J. Tildesley ◽  
G. Saville
Keyword(s):  
Molecular Dynamics ◽  
Multiple Time ◽  
Time Step ◽  
Multiple Time Step

scholarly journals Multiple time step integrators in ab initio molecular dynamics

2014 ◽  
Vol 140 (8) ◽  
pp. 084116 ◽  
Author(s):  
Nathan Luehr ◽  
Thomas E. Markland ◽  
Todd J. Martínez
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Multiple Time ◽  
Time Step ◽  
Multiple Time Step
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