The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Metadynamics
Open accessAbstract
Metadynamics is a powerful technique for enhancing sampling in molecular dynamics simulations and reconstructing the free‐energy surface as a function of few selected degrees of freedom, often referred to as collective variables (CVs). In metadynamics, sampling is accelerated by a history‐dependent bias potential, which is adaptively constructed in the space of the CVs. Since its first appearance, significant improvements have been made to the original algorithm, leading to an efficient, flexible, and accurate method that has found many successful applications in several domains of science. Here, we discuss first the theory underlying metadynamics and its recent developments. In particular, we focus on the crucial issue of choosing an appropriate set of CVs and on the possible strategies to alleviate this difficulty. Later in the second part, we present a few recent representative applications, which we have classified into three main classes: solid‐state physics, chemical reactions, and biomolecules. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 826‐843 DOI: 10.1002/wcms.31 This article is categorized under: Molecular and Statistical Mechanics > Free Energy Methods
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Cites
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
Self-citationAssessing the Accuracy of Metadynamics
Laio, A., Rodriguez-Fortea, A., Gervasio, F. L., Ceccarelli, M., & Parrinello, M. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045424k · Cited by 517
Self-citationThe Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin
Bonomi, M., Branduardi, D., Gervasio, F. L., & Parrinello, M. (2008) · Journal of the American Chemical Society · doi:10.1021/ja803652f · Cited by 97
Self-citationPiana, S., Laio, A., Marinelli, F., Van Troys, M., Bourry, D., Ampe, C., & Martins, J. C. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.10.020 · Cited by 48
Cited by
Unke, O. T., Chmiela, S., Sauceda, H. E., Gastegger, M., Poltavsky, I., Schütt, K. T., Tkatchenko, A., & Müller, K.-R. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01111 · Cited by 1,647
Enhanced sampling techniques in molecular dynamics simulations of biological systems
Bernardi, R. C., Melo, M. C. R., & Schulten, K. (2015) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.10.019 · Cited by 757
Tiwary, P., & Parrinello, M. (2013) · Physical Review Letters · doi:10.1103/physrevlett.111.230602 · Cited by 494
Self-citationVariational Approach to Enhanced Sampling and Free Energy Calculations
Valsson, O., & Parrinello, M. (2014) · Physical Review Letters · doi:10.1103/physrevlett.113.090601 · Cited by 336
Self-citationRandom heteropolymers preserve protein function in foreign environments
Panganiban, B., Qiao, B., Jiang, T., DelRe, C., Obadia, M. M., Nguyen, T. D., Smith, A. A. A., Hall, A., Sit, I., Crosby, M. G., et al. (2018) · Science · doi:10.1126/science.aao0335 · Cited by 294
Metadata
- Authors
- Barducci, A., Bonomi, M., & Parrinello, M.
- Venue
- WIREs Computational Molecular Science
- Publisher
- Wiley
- Published
- 2011-02-18
- Volume
- 1
- Issue
- 5
- Pages
- 826-843
- ISSN
- 1759-0876 (ISSN-L)
- 1759-0884
- OpenAlex
- W4255584963
- Cited by
- 1,180
- References
- 5
- FWCI
- 19.51
- Type
- journal article
- Language
- en
- Open access
- bronze
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