Replica-exchange molecular dynamics: Difference between revisions
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*[http://dx.doi.org/10.1063/1.3249608 Edina Rosta and Gerhard Hummer "Error and efficiency of replica exchange molecular dynamics simulations", Journal of Chemical Physics '''131''' 165102 (2009)] | *[http://dx.doi.org/10.1063/1.3249608 Edina Rosta and Gerhard Hummer "Error and efficiency of replica exchange molecular dynamics simulations", Journal of Chemical Physics '''131''' 165102 (2009)] | ||
*[http://dx.doi.org/10.1063/1.3432176 Jaegil Kim, Thomas Keyes, and John E. Straub "Generalized Replica Exchange Method", Journal of Chemical Physics '''132''' 224107 (2010)] | *[http://dx.doi.org/10.1063/1.3432176 Jaegil Kim, Thomas Keyes, and John E. Straub "Generalized Replica Exchange Method", Journal of Chemical Physics '''132''' 224107 (2010)] | ||
*[http://dx.doi.org/10.1063/1.3533236 Maksim Kouza and Ulrich H. E. Hansmann "Velocity scaling for optimizing replica exchange molecular dynamics", Journal of Chemical Physics '''134''' 044124 (2011)]</ref> | |||
[[Category: Computer simulation techniques]] | [[Category: Computer simulation techniques]] | ||
Revision as of 12:48, 1 February 2011
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Replica-exchange molecular dynamics (REMD) [1] is a tempering method. In this method several replicas of the system are simulated at different temperatures. Every once in a while copies of the system are exchanged.
Thermostats
It has recently been pointed pointed out that one should be very careful which thermostat one employs, the wrong choice leading to non-ergodic behaviour [2]. One should use a canonical ensemble thermostat [3].
See also
References
- ↑ Yuji Sugita and Yuko Okamoto "Replica-exchange molecular dynamics method for protein folding", Chemical Physics Letters 314 pp. 141-151 (1999)
- ↑ Ben Cooke and Scott C. Schmidler "Preserving the Boltzmann ensemble in replica-exchange molecular dynamics", Journal of Chemical Physics 129 164112 (2008)
- ↑ Edina Rosta, Nicolae-Viorel Buchete and Gerhard Hummer "Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations", Journal of Chemical Theory and Computation 5 pp. 1393-1399 (2009)
Related reading
- Hiqmet Kamberaj and Arjan van der Vaart "An optimized replica exchange molecular dynamics method", Journal of Chemical Physics 130 074906 (2009)
- Edina Rosta and Gerhard Hummer "Error and efficiency of replica exchange molecular dynamics simulations", Journal of Chemical Physics 131 165102 (2009)
- Jaegil Kim, Thomas Keyes, and John E. Straub "Generalized Replica Exchange Method", Journal of Chemical Physics 132 224107 (2010)
- Maksim Kouza and Ulrich H. E. Hansmann "Velocity scaling for optimizing replica exchange molecular dynamics", Journal of Chemical Physics 134 044124 (2011)</ref>