Replica-exchange molecular dynamics - Revision history

Carl McBride: /* References */ Added a recent publication

2015-09-21T16:13:42Z

References: Added a recent publication

← Older revision		Revision as of 18:13, 21 September 2015
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	*[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>		*[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]]

Carl McBride: /* References */ Added a recent publication

2011-02-01T10:48:43Z

References: Added a recent publication

← Older revision		Revision as of 12:48, 1 February 2011
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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]]

Carl McBride: /* References */ Added a recent publication

2010-06-14T09:47:04Z

References: Added a recent publication

← Older revision		Revision as of 11:47, 14 June 2010
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	*[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/10.1063/1.3249608 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)]

	[[Category: Computer simulation techniques]]		[[Category: Computer simulation techniques]]

Carl McBride: Started section on thermostats.

2010-02-16T11:55:38Z

Started section on thermostats.

← Older revision		Revision as of 13:55, 16 February 2010
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	{{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) <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/>

Carl McBride: Added a new reference.

2009-10-29T15:28:33Z

Added a new reference.

← Older revision		Revision as of 17:28, 29 October 2009
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	{{stub-general}}		{{stub-general}}
	'''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]].
	==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~~)]		<references/>
	#[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)]		'''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)]
	[[Category: Computer simulation techniques]]		[[Category: Computer simulation techniques]]

Nice and Tidy: /* References */ Added a new reference.

2009-02-24T10:27:36Z

References: Added a new reference.

← Older revision		Revision as of 12:27, 24 February 2009
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	==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)]		#[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)]
			#[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)]
	[[Category: Computer simulation techniques]]		[[Category: Computer simulation techniques]]

Nice and Tidy: 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...

2009-01-17T17:16:25Z

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...

New page

{{stub-general}}
'''Replica-exchange molecular dynamics''' (REMD) is a [[Tempering methods | tempering method]].
==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)]
[[Category: Computer simulation techniques]]