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Items: 1 to 20 of 85

1.

Bayesian estimation of free energies from equilibrium simulations.

Habeck M.

Phys Rev Lett. 2012 Sep 7;109(10):100601. Epub 2012 Sep 4.

PMID:
23005272
2.

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

Ding X, Vilseck JZ, Hayes RL, Brooks CL 3rd.

J Chem Theory Comput. 2017 Jun 13;13(6):2501-2510. doi: 10.1021/acs.jctc.7b00204. Epub 2017 May 26.

3.

Structural analysis of high-dimensional basins of attraction.

Martiniani S, Schrenk KJ, Stevenson JD, Wales DJ, Frenkel D.

Phys Rev E. 2016 Sep;94(3-1):031301. Epub 2016 Sep 15.

PMID:
27739758
4.
5.

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics.

Fajer M, Swift RV, McCammon JA.

J Comput Chem. 2009 Aug;30(11):1719-25. doi: 10.1002/jcc.21285.

7.

Improved estimation of density of states for Monte Carlo sampling via MBAR.

Xu Y, Rodger PM.

J Chem Theory Comput. 2015 Oct 13;11(10):4565-72. doi: 10.1021/acs.jctc.5b00189. Epub 2015 Sep 1.

PMID:
26574248
8.

Calculation of the Gibbs free energy of solvation and dissociation of HCl in water via Monte Carlo simulations and continuum solvation models.

McGrath MJ, Kuo IF, Ngouana W BF, Ghogomu JN, Mundy CJ, Marenich AV, Cramer CJ, Truhlar DG, Siepmann JI.

Phys Chem Chem Phys. 2013 Aug 28;15(32):13578-85. doi: 10.1039/c3cp51762d.

PMID:
23831584
9.

Improving the efficiency of extended ensemble simulations: the accelerated weight histogram method.

Lidmar J.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 May;85(5 Pt 2):056708. Epub 2012 May 25.

PMID:
23004904
10.

BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method.

Ferguson AL.

J Comput Chem. 2017 Jul 5;38(18):1583-1605. doi: 10.1002/jcc.24800. Epub 2017 May 5.

PMID:
28475830
11.

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions.

Paliwal H, Shirts MR.

J Chem Theory Comput. 2013 Nov 12;9(11):4700-17. doi: 10.1021/ct4005068. Epub 2013 Oct 17.

PMID:
26583389
12.
13.

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace.

Zhang C, Lai CL, Pettitt BM.

Mol Simul. 2016;42(13):1079-1089. Epub 2016 Jul 5.

14.

A Stochastic Solution to the Unbinned WHAM Equations.

Zhang BW, Xia J, Tan Z, Levy RM.

J Phys Chem Lett. 2015 Oct 1;6(19):3834-40. doi: 10.1021/acs.jpclett.5b01771. Epub 2015 Sep 14.

15.

Monte Carlo simulations for the free energies of C60 and C70 fullerene crystals by acceptance ratio method and expanded ensemble method.

Kim M, Chang J, Sandler SI.

J Chem Phys. 2014 Feb 28;140(8):084110. doi: 10.1063/1.4866451.

PMID:
24588151
16.

Conformational free energies of 1,2-dichloroethane in nanoconfined methanol.

Gomez JA, Tucker AK, Shepherd TD, Thompson WH.

J Phys Chem B. 2005 Sep 22;109(37):17479-87.

PMID:
16853235
17.

Statistically optimal analysis of samples from multiple equilibrium states.

Shirts MR, Chodera JD.

J Chem Phys. 2008 Sep 28;129(12):124105. doi: 10.1063/1.2978177.

18.

Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).

Hafner J.

J Phys Condens Matter. 2008 Feb 13;20(6):060301. doi: 10.1088/0953-8984/20/06/060301. Epub 2008 Jan 24.

PMID:
21693862
19.

Bayesian inference based on stationary Fokker-Planck sampling.

Berrones A.

Neural Comput. 2010 Jun;22(6):1573-96. doi: 10.1162/neco.2010.01-09-943.

PMID:
20141472
20.

Gibbs sampling for time-delay-and amplitude estimation in underwater acoustics.

Michalopoulou ZH, Picarelli M.

J Acoust Soc Am. 2005 Feb;117(2):799-808.

PMID:
15759700

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