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Literature DB >> 16821906

Analysis of the statistical error in umbrella sampling simulations by umbrella integration.

Abstract

Umbrella sampling simulations, or biased molecular dynamics, can be used to calculate the free-energy change of a chemical reaction. We investigate the sources of different sampling errors and derive approximate expressions for the statistical errors when using harmonic restraints and umbrella integration analysis. This leads to generally applicable rules for the choice of the bias potential and the sampling parameters. Numerical results for simulations on an analytical model potential are presented for validation. While the derivations are based on umbrella integration analysis, the final error estimate is evaluated from the raw simulation data, and it may therefore be generally applicable as indicated by tests using the weighted histogram analysis method.

Year: 2006 PMID： 16821906 DOI： 10.1063/1.2206775

Source DB: PubMed Journal: J Chem Phys ISSN： 0021-9606 Impact factor: 3.488

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Cited

18 in total

1. Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations.

Authors: Dhruva K Chakravorty; Sharon Hammes-Schiffer
Journal: J Am Chem Soc Date: 2010-06-02 Impact factor: 15.419

10. Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics.

Authors: Dhruva K Chakravorty; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal: Biochemistry Date: 2009-11-10 Impact factor: 3.162

Analysis of the statistical error in umbrella sampling simulations by umbrella integration.

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