Literature DB >> 17930362

Simulation via direct computation of partition functions.

Cheng Zhang1, Jianpeng Ma.   

Abstract

In this paper, we demonstrate the efficiency of simulations via direct computation of the partition function under various macroscopic conditions, such as different temperatures or volumes. The method can compute partition functions by flattening histograms, through, for example, the Wang-Landau recursive scheme, outside the energy space. This method offers a more general and flexible framework for handling various types of ensembles, especially ones in which computation of the density of states is not convenient. It can be easily scaled to large systems, and it is flexible in incorporating Monte Carlo cluster algorithms or molecular dynamics. High efficiency is shown in simulating large Ising models, in finding ground states of simple protein models, and in studying the liquid-vapor phase transition of a simple fluid. The method is very simple to implement and we expect it to be efficient in studying complex systems with rugged energy landscapes, e.g., biological macromolecules.

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Year:  2007        PMID: 17930362      PMCID: PMC3133746          DOI: 10.1103/PhysRevE.76.036708

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  19 in total

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6.  Critical point estimation of the Lennard-Jones pure fluid and binary mixtures.

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7.  Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models.

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Authors:  M Scott Shell; Pablo G Debenedetti; Athanassios Z Panagiotopoulos
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-07-23

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  15 in total

1.  Estimating statistical distributions using an integral identity.

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Authors:  Jaegil Kim; Thomas Keyes; John E Straub
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4.  Enhanced sampling and applications in protein folding in explicit solvent.

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5.  Fast, fully Bayesian spatiotemporal inference for fMRI data.

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6.  Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.

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7.  Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2009-05-21       Impact factor: 3.488

8.  Comparison of sampling efficiency between simulated tempering and replica exchange.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2008-10-07       Impact factor: 3.488

9.  Optimal replica exchange method combined with Tsallis weight sampling.

Authors:  Jaegil Kim; John E Straub
Journal:  J Chem Phys       Date:  2009-04-14       Impact factor: 3.488

10.  Folding helical proteins in explicit solvent using dihedral-biased tempering.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-09       Impact factor: 11.205

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