A dynamical monte carlo algorithm for master equations with time-dependent transition rates

1997 ◽  
Vol 89 (3-4) ◽  
pp. 709-734 ◽  
Author(s):  
A. Prados ◽  
J. J. Brey ◽  
B. Sánchez-Rey
Keyword(s):  
Monte Carlo ◽  
Master Equations ◽  
Time Dependent ◽  
Monte Carlo Algorithm ◽  
Transition Rates

Examining sharp restart in a Monte Carlo method for the linearized Poisson–Boltzmann equation

2020 ◽  
Vol 26 (3) ◽  
pp. 223-244
Author(s):  
W. John Thrasher ◽  
Michael Mascagni
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Algorithm ◽  
Significant Bias ◽  
Poisson Boltzmann ◽  
Electrostatic Free Energy ◽  
Poisson Boltzmann Equation ◽  
The Stability ◽  
Potential Methods ◽  
The Individual

AbstractIt has been shown that when using a Monte Carlo algorithm to estimate the electrostatic free energy of a biomolecule in a solution, individual random walks can become entrapped in the geometry. We examine a proposed solution, using a sharp restart during the Walk-on-Subdomains step, in more detail. We show that the point at which this solution introduces significant bias is related to properties intrinsic to the molecule being examined. We also examine two potential methods of generating a sharp restart point and show that they both cause no significant bias in the examined molecules and increase the stability of the run times of the individual walks.

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