Bridge Sampling, Importance Sampling and Incremental Umbrella Sampling

Related but not often put into relation:

- Weighted histogram analysis method

- Estimation of normalizing constants

- Importance sampling

- Umbrella sampling

- Incremental umbrella sampling

- Bridge sampling

- Path sampling

A Start of a Collection of Links

Towards Bridge Sampling

Empirical distributions in selection bias models

Y Vardi, 1985

The Annals of Statistics 13 (1) 178-203

Estimating normalizing constants and reweighting mixtures in Markov chain Monte Carlo

[PDF] à partir de psu.edu

CJ Geyer, 1994

Technical Report 568, 1994

Simulating ratios of normalizing constants via a simple identity: a theoretical exploration
XL Meng, WH Wong, 1996
Statistica Sinica 6, 831-860

Simulating normalizing constants: From importance sampling to bridge sampling to path sampling
A Gelman, XL Meng, 1998
Statistical Science, 163-185

A theory of statistical models for Monte Carlo integration
A Kong, P McCullagh, XL Meng, D Nicolae, Z Tan, 2003
Journal of the Royal Statistical Society: Series B (Statistical Methodology)

A theory of statistical models for Monte Carlo integration
A Kong, P McCullagh, XL Meng, D Nicolae, Z Tan, 2003
Journal of the Royal Statistical Society: Series B (Statistical Methodology) 

On a likelihood approach for Monte Carlo integration

[PDF] à partir de amstat.org

Z Tan, 2004

Journal of the American Statistical Association 99 (468) 1027-1036

Towards Incremental Umbrella Sampling

The weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

[PDF] à partir de sabanciuniv.edu

S Kumar, JM Rosenberg, D Bouzida, RH Swendsen, PA Kollman, 1992

Journal of Computation Chemistry, 13 (8) 1011-1021

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
C Bartels, M Karplus, 1997
Journal of computational chemistry 18 (12), 1450-1462

Analyzing biased Monte Carlo and molecular dynamics simulations
C Bartels, 2000
Chemical Physics Letters 331 (5-6), 446-454

Absolute free energies of binding of peptide analogs to the HIV‐1 protease from molecular dynamics simulations
C Bartels, A Widmer, C Ehrhardt, 2005
Journal of computational chemistry 26 (12), 1294-1305

Some Attempts to Digest

Statistically optimal analysis of samples from multiple equilibrium states

MR Shirts, JD Chodera, 2008

The Journal of chemical physics 129 (124105)

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures
JD Chodera, WC Swope, F Noé, JH Prinz, MR Shirts, VS Pande, 2011
The Journal of chemical physics 134, 244107