Integration Methods for Molecular Dynamics

1996 ◽  
pp. 161-185 ◽  
Author(s):  
Benedict J. Leimkuhler ◽  
Sebastian Reich ◽  
Robert D. Skeel
Keyword(s):  
Molecular Dynamics ◽  
Integration Methods

Novel Gear-like predictor–corrector integration methods for molecular dynamics

2019 ◽  
Vol 118 (9-10) ◽  
pp. e1674937
Author(s):  
Jiří Janek ◽  
Jiří Kolafa
Keyword(s):  
Molecular Dynamics ◽  
Integration Methods ◽  
Predictor Corrector

scholarly journals High-order time integration methods in molecular dynamics

PAMM ◽  
2012 ◽  
Vol 12 (1) ◽  
pp. 47-48 ◽  
Author(s):  
Florian Niederhöfer ◽  
Jens Wackerfuß
Keyword(s):  
Molecular Dynamics ◽  
Time Integration ◽  
High Order ◽  
Integration Methods ◽  
Time Integration Methods ◽  
High Order Time

Implicit Integration in Molecular Dynamics Simulation

2008 ◽  
Author(s):  
Nicholas P. Schafer ◽  
Radu Serban ◽  
Dan Negrut
Keyword(s):  
Molecular Dynamics ◽  
Newton Method ◽  
Dynamics Simulation ◽  
Integration Scheme ◽  
Implicit Integration ◽  
Step Size ◽  
Time Step ◽  
Integration Methods ◽  
Size Limitation ◽  
Quasi Newton

Molecular Dynamics (MD) simulation is a versatile methodology that has found many applications in materials science, chemistry and biology. In biology, the models employed range from mixed quantum mechanical and fully atomistic to united atom and continuum mechanical. These systems are evolved in discrete time by solving Newton’s equations of motion at each time step. The numerical methods currently in use limit the step size of a typical all atom simulation to 1 femtosecond. This step size limitation means that many steps need to be taken in order to reach biologically relevant time scales. At each time step, an evaluation of the forces on each atom must be performed resulting in heavy computational loads. This work investigates the use of implicit integration methods in MD. Implicit integration methods have been proven superior to their explicit counterparts in classical mechanical simulation, with which MD has many similarities. Longer time steps reduce the number of force evaluations that must be performed and the corresponding computational load. Herein we present results that compare implicit integration techniques with the current standard for molecular dynamics, the explicit velocity Verlet integration scheme. Total energy conservation is used as a metric for evaluating the dependability of simulations in the microcanonical ensemble. In order to understand the nature of the problem, several long simulations were run and analyzed by performing a Fourier analysis on the position, velocity and acceleration signals. Lastly, several methods for improving the viability of implicit integration methods are considered including replacing the Jacobian used in the Quasi-Newton method with a constant, diagonal mass matrix, evaluating the Jacobian infrequently and finding a better prediction of the system configuration to improve the convergence of the Quasi-Newton method.

Error and timing analysis of multiple time-step integration methods for molecular dynamics

2007 ◽  
Vol 176 (4) ◽  
pp. 271-291 ◽  
Author(s):  
Guowen Han ◽  
Yuefan Deng ◽  
James Glimm ◽  
Glenn Martyna
Keyword(s):  
Molecular Dynamics ◽  
Timing Analysis ◽  
Multiple Time ◽  
Time Step ◽  
Integration Methods ◽  
Multiple Time Step

Nonequilibrium Molecular Dynamics

2017 ◽  
Author(s):  
Billy D. Todd ◽  
Peter J. Daivis
Keyword(s):  
Molecular Dynamics ◽  
Nonequilibrium Molecular Dynamics

Molecular dynamics of cyclohexane guest molecules in the cyclohexane/thiourea inclusion compound: an incoherent quasielastic neutron scattering investigation

1998 ◽  
Vol 93 (4) ◽  
pp. 545-554 ◽  
Author(s):  
MATTHEW JONES ◽  
FRANCOIS GUILLAUME ◽  
KENNETH HARRIS ◽  
ABIL ALIEV ◽  
PASCALE GIRARD ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Inclusion Compound ◽  
Guest Molecules ◽  
Quasielastic Neutron ◽  
Quasielastic Neutron Scattering
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