The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
Enhanced Sampling in the Well-Tempered Ensemble
Open accessAbstract
We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi, J. Comput. Chem. 30, 1615 (2009)]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a Gō model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.
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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct700301q · Cited by 15,908
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
Self-citationUnderstanding Molecular Simulation
Frenkel, D., Smit, B., Tobochnik, J., McKay, S. R., & Christian, W. (1997) · Computers in Physics · doi:10.1063/1.4822570 · Cited by 5,395
Nonequilibrium Equality for Free Energy Differences
Jarzynski, C. (1997) · Physical Review Letters · doi:10.1103/physrevlett.78.2690 · Cited by 5,293
Replica-exchange molecular dynamics method for protein folding
Sugita, Y., & Okamoto, Y. (1999) · Chemical Physics Letters · doi:10.1016/s0009-2614(99)01123-9 · Cited by 4,514
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
Barducci, A., Bussi, G., & Parrinello, M. (2008) · Physical Review Letters · doi:10.1103/physrevlett.100.020603 · Cited by 3,184
Self-citationEfficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States
Wang, F., & Landau, D. P. (2001) · Physical Review Letters · doi:10.1103/physrevlett.86.2050 · Cited by 2,896
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
Bolhuis, P. G., Chandler, D., Dellago, C., & Geissler, P. L. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.082301.113146 · Cited by 1,972
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., et al. (2009) · Computer Physics Communications · doi:10.1016/j.cpc.2009.05.011 · Cited by 1,875
Self-citationSimulated Tempering: A New Monte Carlo Scheme
Marinari, E., & Parisi, G. (1992) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/19/6/002 · Cited by 1,818
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Tiwary, P., & Parrinello, M. (2013) · Physical Review Letters · doi:10.1103/physrevlett.111.230602 · Cited by 494
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Metadata
- Authors
- Bonomi, M., & Parrinello, M.
- Venue
- Physical Review Letters
- Publisher
- American Physical Society (APS)
- Published
- 2010-05-10
- Volume
- 104
- Issue
- 19
- Pages
- 190601-190601
- ISSN
- 0031-9007 (ISSN-L)
- 1079-7114
- OpenAlex
- W2071360373
- Cited by
- 273
- References
- 29
- FWCI
- 7.38
- Type
- journal article
- Language
- en
- Open access
- green
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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