Latest revision |
Your text |
Line 1: |
Line 1: |
| {{stub-general}} | | {{stub-general}} |
| '''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]]. | | '''Replica-exchange molecular dynamics''' (REMD) 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/>
| | #[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)] |
| '''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/10.1063/1.3077857 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]] |