Sunday, April 15, 2012

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

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

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
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




SAMPLING METHOD
C BARTELS, 2004
WO Patent WO/2004/021,208


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


Incremental umbrella sampling
C Bartels, 2011
US Patent 7,987,219

Some Attempts to Digest


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

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