Replica-exchange molecular dynamics: Difference between revisions
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m (New page: {{stub-general}} '''Replica-exchange molecular dynamics''' (REMD) is a tempering method. ==References== #[http://dx.doi.org/10.1016/S0009-2614(99)01123-9 Yuji Sugi...) |
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'''Replica-exchange molecular dynamics''' (REMD) is a [[Tempering methods | tempering method]]. | '''Replica-exchange molecular dynamics''' (REMD) <ref>[http://dx.doi.org/10.1016/S0009-2614(99)01123-9 Yuji Sugita and Yuko Okamoto "Replica-exchange molecular dynamics method for protein folding", Chemical Physics Letters '''314''' pp. 141-151 (1999)]</ref> is a [[Tempering methods | tempering method]]. | ||
In this method several replicas of the system are simulated at different [[temperature]]s. 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 [[thermostats | thermostat]] one employs, the wrong choice leading to [[Ergodic hypothesis | non-ergodic]] behaviour <ref>[http://dx.doi.org/10.1063/1.2989802 Ben Cooke and Scott C. Schmidler "Preserving the Boltzmann ensemble in replica-exchange molecular dynamics", Journal of Chemical Physics '''129''' 164112 (2008)]</ref>. One should use a [[canonical ensemble]] thermostat | |||
<ref>[http://dx.doi.org/10.1021/ct800557h 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)]</ref>. | |||
==See also== | |||
*[[Parallel tempering]] | |||
==References== | ==References== | ||
<references/> | |||
'''Related reading''' | |||
*[http://dx.doi.org/10.1063/1.3077857 Hiqmet Kamberaj and Arjan van der Vaart "An optimized replica exchange molecular dynamics method", Journal of Chemical Physics '''130''' 074906 (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/10.1063/1.3533236 Maksim Kouza and Ulrich H. E. Hansmann "Velocity scaling for optimizing replica exchange molecular dynamics", Journal of Chemical Physics '''134''' 044124 (2011)]</ref> | |||
*[http://dx.doi.org/10.1063/1.4926937 Zhixiong Lin and Wilfred F. van Gunsteren "On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations", Journal of Chemical Physics '''143''' 034110 (2015)] | |||
[[Category: Computer simulation techniques]] | [[Category: Computer simulation techniques]] | ||
Latest revision as of 18:13, 21 September 2015
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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[edit]
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[edit]
References[edit]
- ↑ 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>
- Zhixiong Lin and Wilfred F. van Gunsteren "On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations", Journal of Chemical Physics 143 034110 (2015)