Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration".

By J. Kästner, Walter Thiel. Journal of Chemical Physics, 2005

397 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e528685ce7da8bc9d538feaa1203d7edc1a6ec16

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Atomic and Molecular Physics, and Optics

1. ST John
2. Cameron F. Abrams
3. Tony Lelièvre
4. J'erome H'enin
5. Giovanni Bussi
6. Gábor Csányi
7. Lucie Delemotte
8. Omar Valsson

In Biomedical Engineering

1. ST John
2. Cameron F. Abrams
3. Stefano Moro
4. Tony Lelièvre
5. Gábor Csányi
6. Giovanni Bussi
7. David B. Graves
8. Veronica Salmaso

In Molecular Biology

1. J'erome H'enin
2. Tony Lelièvre
3. Mark J. Kushner
4. Omar Valsson
5. Lucie Delemotte
6. Cameron F. Abrams
7. Michael R. Shirts
8. Gábor Csányi

Citations in the corpus

• Plasma–liquid interactions: a review and roadmap (2016, methodology): “method [176] or umbrella integration [177] which enable”
• Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “The implementation of eABF in the Colvars Module [229] is complemented by two free energy estimators, the corrected zaveraged restraint (CZAR) [229], and an Umbrella Integration estimator [228, 230, 231].”
• Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. (2016, methodology): “The most popular methods are the gradient-based Umbrella Integration [67, 68], the Blue Moon method [69, 70], the Adaptive Biasing Force (ABF) method [71, 72], and the histogram-based Metadynamics [73–75].”
• Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration (2013, methodology): “An alternative to WHAM, termed “umbrella integration”, solves the problem of renormalization across windows by constructing the composite mean force [71,72].”
• Water and ions in clays: Unraveling the interlayer/micropore exchange using molecular dynamics (2007, methodology): “The error on the Umbrella Integration results can be evaluated using the method of Kästner and Thiel [Kästner and Thiel, 2006].”
• Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, methodology): “…methods can be used to perform combination and analysis of the data coming from the different US windows; the most famous is umbrella integration (Kästner and Thiel, 2005), the weighted histogram analysis method (WHAM) (Kumar et al., 1992), and the more recent Dynamic Weighted Histogram Analysis…”