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Replica exchange with solute tempering: A method for sampling biological systems in explicit water
Open accessAbstract
An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST is compared with standard replica exchange for an alanine dipeptide molecule in water. The comparisons confirm that REST greatly reduces the number of CPUs required by regular replica exchange and increases the sampling efficiency. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water.
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Cited by
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Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Wang, L., Wu, Y., Deng, Y., Kim, B., Pierce, L., Krilov, G., Lupyan, D., Robinson, S., Dahlgren, M. K., Greenwood, J., et al. (2015) · Journal of the American Chemical Society · doi:10.1021/ja512751q · Cited by 1,313
Self-citationPolarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
Lopes, P. E. M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., & MacKerell, A. D. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400781b · Cited by 386
Seabra, G. D. M., Walker, R. C., Elstner, M., Case, D. A., & Roitberg, A. E. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp070071l · Cited by 257
Abrams, J. B., & Tuckerman, M. E. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp805039u · Cited by 221
Metadata
- Authors
- Liu, P., Kim, B., Friesner, R. A., & Berne, B. J.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2005-09-19
- Volume
- 102
- Issue
- 39
- Pages
- 13749-13754
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2146942655
- Cited by
- 805
- References
- 0
- FWCI
- 6.91
- Type
- journal article
- Language
- en
- Open access
- green
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- Liu, P., Kim, B., Friesner, R. A., & Berne, B. J. (2005). Replica exchange with solute tempering: A method for sampling biological systems in explicit water. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0506346102
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