A constrained hybrid Monte-Carlo algorithm and the problem of calculating the free energy in several variables

2005 ◽  
Vol 85 (10) ◽  
pp. 700-710 ◽  
Author(s):  
C. Hartmann ◽  
C. Schütte
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Algorithm ◽  
Hybrid Monte Carlo ◽  
Several Variables

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.

scholarly journals Testing a Fourier-accelerated hybrid Monte Carlo algorithm

2002 ◽  
Vol 528 (3-4) ◽  
pp. 301-305 ◽  
Author(s):  
Simon Catterall ◽  
Sergey Karamov
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Algorithm ◽  
Hybrid Monte Carlo

scholarly journals COMPARISON OF UPDATE ALGORITHMS FOR PURE GAUGE SU(3)

1988 ◽  
Vol 03 (14) ◽  
pp. 1367-1378 ◽  
Author(s):  
RAJAN GUPTA ◽  
GREGORY W. KILCUP ◽  
APOORVA PATEL ◽  
STEPHEN R. SHARPE ◽  
PHILIPPE DE FORCRAND
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Algorithm ◽  
Hybrid Monte Carlo ◽  
Pure Gauge

We show that the overrelaxed algorithm of Creutz and of Brown and Woch is the optimal local update algorithm for simulation of pure gauge SU(3). Our comparison criterion includes computer efficiency and decorrelation times. We also investigate the rate of decorrelation for the Hybrid Monte Carlo algorithm.

Nucleation free-energy barriers with Hybrid Monte-Carlo/Umbrella Sampling

2014 ◽  
Vol 16 (45) ◽  
pp. 24913-24919 ◽  
Author(s):  
M. A. Gonzalez ◽  
E. Sanz ◽  
C. McBride ◽  
J. L. F. Abascal ◽  
C. Vega ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Umbrella Sampling ◽  
Energy Barriers ◽  
Hybrid Monte Carlo

scholarly journals Measure of autocorrelation times of local hybrid Monte Carlo algorithm for lattice QCD

1993 ◽  
Vol 315 (1-2) ◽  
pp. 152-156 ◽  
Author(s):  
Paolo Marenzoni ◽  
Luigi Pugnetti ◽  
Pietro Rossi
Keyword(s):  
Monte Carlo ◽  
Lattice Qcd ◽  
Monte Carlo Algorithm ◽  
Hybrid Monte Carlo

scholarly journals Berezinskii-Kosterlitz-Thouless phase transition from lattice sine-Gordon model

2018 ◽  
Vol 175 ◽  
pp. 14003
Author(s):  
Joel Giedt ◽  
James Flamino
Keyword(s):  
Phase Transition ◽  
Monte Carlo ◽  
Critical Temperature ◽  
Finite Size ◽  
Monte Carlo Algorithm ◽  
Finite Size Scaling ◽  
Hybrid Monte Carlo ◽  
Lattice Field ◽  
Autocorrelation Time ◽  
Sine Gordon Model

We obtain nonperturbative results on the sine-Gordon model using the lattice field technique. In particular, we employ the Fourier accelerated hybrid Monte Carlo algorithm for our studies. We find the critical temperature of the theory based autocorrelation time, as well as the finite size scaling of the “thickness” observable used in an earlier lattice study by Hasenbusch et al.

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