Replica-exchange molecular dynamics: Difference between revisions
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'''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) <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/> | <references/> | ||
Revision as of 12:55, 16 February 2010
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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)
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