Literature DB >> 15244974

Adaptive integration method for Monte Carlo simulations.

Marc Fasnacht1, Robert H Swendsen, John M Rosenberg.   

Abstract

We present an adaptive sampling method for computing free energies, radial distribution functions, and potentials of mean force. The method is characterized by simplicity and accuracy, with the added advantage that the data are obtained in terms of quasicontinuous functions. The method is illustrated and tested with simulations on a high density fluid, including a stringent consistency test involving an unusual thermodynamic cycle that highlights its advantages.

Mesh:

Year:  2004        PMID: 15244974     DOI: 10.1103/PhysRevE.69.056704

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


  10 in total

1.  Generalized simulated tempering for exploring strong phase transitions.

Authors:  Jaegil Kim; John E Straub
Journal:  J Chem Phys       Date:  2010-10-21       Impact factor: 3.488

2.  Enhanced sampling and applications in protein folding in explicit solvent.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2010-06-28       Impact factor: 3.488

3.  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

Review 4.  Equilibrium sampling in biomolecular simulations.

Authors:  Daniel M Zuckerman
Journal:  Annu Rev Biophys       Date:  2011       Impact factor: 12.981

5.  Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.

Authors:  Steven Lettieri; Artem B Mamonov; Daniel M Zuckerman
Journal:  J Comput Chem       Date:  2010-11-29       Impact factor: 3.376

6.  Two-phase dynamics of DNA supercoiling based on DNA polymer physics.

Authors:  Biao Wan; Jin Yu
Journal:  Biophys J       Date:  2022-01-10       Impact factor: 4.033

Review 7.  Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.

Authors:  Hagai Meirovitch; Srinath Cheluvaraja; Ronald P White
Journal:  Curr Protein Pept Sci       Date:  2009-06       Impact factor: 3.272

8.  Enhanced ligand sampling for relative protein-ligand binding free energy calculations.

Authors:  Joseph W Kaus; J Andrew McCammon
Journal:  J Phys Chem B       Date:  2015-05-08       Impact factor: 2.991

9.  Accelerated adaptive integration method.

Authors:  Joseph W Kaus; Mehrnoosh Arrar; J Andrew McCammon
Journal:  J Phys Chem B       Date:  2014-05-06       Impact factor: 2.991

10.  Implementation of adaptive integration method for free energy calculations in molecular systems.

Authors:  Christopher A Mirabzadeh; F Marty Ytreberg
Journal:  PeerJ Comput Sci       Date:  2020-03-16
  10 in total

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