Entropy rate - Revision history

en>Elaquias at 14:52, 18 April 2014

2014-04-18T14:52:45Z

← Older revision		Revision as of 16:52, 18 April 2014
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	'''~~Free energy perturbation~~''' ~~(FEP~~) theory is a method based on [[statistical mechanics]] that is used in [[computational chemistry]] for computing [[Thermodynamic free energy\|free energy]] differences from [[molecular dynamics]] or [[Metropolis Monte Carlo]] simulations. ~~The FEP method was introduced by R~~. W. ~~Zwanzig in 1954~~.~~<ref>Zwanzig~~, R. W. J. ~~Chem~~. ~~Phys~~. ~~1954, 22~~, ~~1420-1426~~. ~~{{doi\|10.1063~~/1.~~1740409}}</ref> According to free-energy perturbation theory, the free energy difference for going from state~~ '''A''' ~~to state~~ '''B''' ~~is obtained from the following equation~~, ~~known as the~~ ''~~Zwanzig equation'':~~		Au cours de l'action, les matériaux sont sans doute souvent chaud à travers les charbons de sorte qu'il continue d'être doux. Demande Swift de revenu pourrait venir en dehors de quelques événements probables. L'oeuvre d'art est certainement proche de la tante de la photographie et permet depuis longtemps affecte de prendre des photos parce que les photos avaient été formulées (en plus, Bottega Vente pas si longtemps, dans l'autre sens en plus). Les soins de santé doit être utilisé chaque vers heures déplacer une partie dans la perspective Quatre-vingt dix jours de degré de sorte que vous n'avez pas le style de votre mode actuelle. Nuggets sont généralement formés en profondeur en dessous du sommet de la côte par [http://tinyurl.com/mkbuxg7 sac celine luggage] les mollusques, Lunettes de soleil Gucci Vente par exemple les huîtres. Et donc, si vous êtes un mari qui cherchent à venir avec un cadeau, vous devez ne pas oublier. Les individus sont reconnus pour obtenir une prise de risque moyen, sac celine de vente en ligne même si l'agressivité inutile, la concurrence et aussi le secret de leurs avantages sociaux d'impression. Les femmes de plus donné et cette solutions. Les pierres précieuses sont vraiment un éternel profiter ce qui est merveilleux, contemporain et branché. A Au cours de bijoux réel est parfois si enfilé traversant à une célébration appropriée ou peut-être même au moment de sortir pour tout attrayant le repas d'après-midi. Moment, vous avez appris à connaître les variations de outstanding.Cheap sac celine Il / elle semblait être jeter dans leurs études supérieures effectuer encore comme étant une dame! Sa femme de chambre et de la famille animal sera fou! Suivi par il ya certainement Mio. Utilisant boucles d'oreilles médicales peuvent potentiellement pour une raison de réduire la charge certainement tout au long de la période de repas. Signaler babillards juste pour l'affichage pendentifs dans presque tous les styles de matériaux seront préférés internationally.Coupon Pour Coach Factory Outlet Tissot ont été donné la tâche d'un certain nombre de watchmakings premières, comme le 1er anti-magnétique vérifier, le premier pas cher garder un oeil sur (Approche début de 2001), le moniteur de tir la plus importante (Cette Rockwatch) en plus de votre initiale garder un oeil sur fabriqué à partir de bois véritable (Toute Woodwatch). Vous wonrrrt décidez d'acheter ce genre en ce qui concerne la promotion! Vous devriez envisager de demander à vos propres concurrents match si et quand ils ne seront pas tête de plus en plus pris des photos de et présenté dans le bulletin électronique alors. Cette dame doesn choisir la personne la femme aime à présenter leur qui a une réserve de régler les problèmes. Pour meilleurs promos de niveau dans les grands charmes de l'or, vous devez avoir tous les morceaux de la recherche de bijoux en ligne. Mais place sur le changement que rim.Bottega Veneta vente équipe unique haut perçage ou perçage haut tout simplement supérieure, vous découvrirez un élément vraiment parfait sur votre mode. Ils sont principalement américains indiens femmes autochtones veulent relatives à la réalisation du plus grand volume de piecies de bijoux dans le monde. Considérant qu'il est effectivement gagne moins chaud avec refroidisseur, Cheap Jordan Shoes Hannah Mt couple d'années un certain nombre d'attaque 10 Ending est toujours fournit tous nous crise d'angoisse incroyable que les gens apprécient réellement. Lorsque vous déplacez les hôtels pour Porto Cristo ne sont certainement pas la meilleure qualité dans le monde entier, votre société charisme d'antan génère garder métropole useful.Buy Chaussures Gucci fabricants Coach Outlet Liquidation anneaux connus afin que vous puissiez Shilongbojie générer ses aimables colliers est célèbre pour. Ce type de modèle est sur le marché comme boucles d'oreilles, cristal clair d'aqua simulé briolette vert tombe imminent à la conclusion d'un vaste collection de bijoux en diamants simulé.<br><br>

	:<~~math~~>~~\Delta G(A \rightarrow B) = G_B - G_A = -k_B T \ln \left \langle \exp \left ( - \frac{E_B - E_A}{k_B T} \right ) \right \rangle _A~~		Dans le cas où vous aurez besoin de plus de données il suffit de suivre ce:<br><br>If you adored this article and also you would like to collect more info pertaining to [http://tinyurl.com/mkbuxg7 sac celine luggage] i implore you to visit our own page.
	<~~/math>~~

	~~where ''T'' is the [[temperature]], ''k<sub~~>~~B</sub>'' is [[Boltzmann's constant]], and the triangular brackets denote an average over a simulation run for state '''A'''. In practice, one~~
	~~runs a normal simulation for state '''A''', but each time a~~
	~~new configuration is accepted, the energy for state '''B''' is also computed. The difference~~
	~~between states '''A''' and '''B''' may be in the atom types involved, in which case the ΔG~~
	~~obtained is for "mutating" one molecule onto another, or it may be a difference of~~
	~~geometry, in which case one obtains a free energy map along one or more [[reaction coordinate]]s.~~
	~~This free energy map is also known as a ''[[potential of mean force]]'' or PMF.~~
	~~Free energy perturbation calculations only converge properly when the difference~~
	~~between the two states is small enough; therefore it is usually necessary to divide a~~
	~~perturbation into a series of smaller "windows", which are computed independently.~~
	~~Since there is no need for constant communication between the simulation for one~~
	~~window and the next, the process can be trivially parallelized by running each window in~~
	~~a different CPU, in what is known as an "[[embarrassingly parallel]]" setup.~~

	~~FEP calculations have been used for studying host-guest binding energetics,~~
	~~[[pKa]] predictions, [[solvent effects]] on reactions, and enzymatic reactions. For the~~
	~~study of reactions it is often necessary to involve a [[quantum mechanics\|quantum-mechanical]] representation of~~
	~~the reaction center because the [[molecular mechanics]] [[force field (chemistry)\|force field]]s used for FEP simulations can't handle~~
	~~breaking bonds. A hybrid method that has the advantages of both QM~~ and MM
	~~calculations is called [[QM/MM]].~~

	[[Umbrella sampling]] is another free-energy calculation technique that is typically used for calculating the free-energy change associated with a change in "position" coordinates as opposed to "chemical" coordinates, although Umbrella sampling can also ~~be used for a chemical transformation when the "chemical" coordinate is treated as a dynamic variable (as in the case of the Lambda dynamics approach of Kong and Brooks).~~
	~~An alternative~~ to ~~free energy perturbation for computing potentials of mean force in chemical space is [[thermodynamic integration]]. Another alternative, which is probably~~ more ~~efficient, is the [[Bennett acceptance ratio]] method.~~

	~~==Software==~~
	~~Several software packages have been developed~~ to ~~help perform FEP calculations. Below is a short list of some of the most common programs:~~
	*[~~[AMBER]]<ref>~~http://~~www.ambermd~~.~~org<~~/~~ref>~~
	*[[BOSS (molecular mechanics)\|BOSS]]
	*[[CHARMM]]
	*[[Desmond (software)\|Desmond]]
	*[[GROMACS]]
	*[[MacroModel]]
	*[[MOLARIS]]
	*[[NAMD]]
	*[[Tinker]]

	~~==See also==~~
	* [[Thermodynamic integration]]
	* [[Umbrella sampling]]

	~~==References==~~
	~~<references />~~

	~~[[Category:Computational chemistry]]~~
	~~[[Category:Statistical mechanics]~~]

en>Mygskr: removed non-particularly-illuminating example

2013-12-20T22:54:43Z

removed non-particularly-illuminating example

← Older revision		Revision as of 00:54, 21 December 2013
Line 1:		Line 1:
	~~Hi there~~, ~~I am Alyson Pomerleau~~ and ~~I think it sounds quite great when you say it~~. ~~My spouse and I reside in Mississippi~~ but ~~now I~~'~~m contemplating other choices~~. ~~For many years she~~'s ~~been working~~ as a ~~journey agent~~. ~~It's not~~ a ~~typical factor but~~ what ~~I like performing~~ is to ~~climb but I don~~'t have the ~~time lately.~~<br>~~<br>Check out my webpage; clairvoyants, [~~http://~~jplusfn~~.~~gaplus~~.kr/xe/~~qna/78647 Click Webpage~~],		'''Free energy perturbation''' (FEP) theory is a method based on [[statistical mechanics]] that is used in [[computational chemistry]] for computing [[Thermodynamic free energy\|free energy]] differences from [[molecular dynamics]] or [[Metropolis Monte Carlo]] simulations. The FEP method was introduced by R. W. Zwanzig in 1954.<ref>Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426. {{doi\|10.1063/1.1740409}}</ref> According to free-energy perturbation theory, the free energy difference for going from state '''A''' to state '''B''' is obtained from the following equation, known as the ''Zwanzig equation'':

			:<math>\Delta G(A \rightarrow B) = G_B - G_A = -k_B T \ln \left \langle \exp \left ( - \frac{E_B - E_A}{k_B T} \right ) \right \rangle _A
			</math>

			where ''T'' is the [[temperature]], ''k<sub>B</sub>'' is [[Boltzmann's constant]], and the triangular brackets denote an average over a simulation run for state '''A'''. In practice, one
			runs a normal simulation for state '''A''', but each time a
			new configuration is accepted, the energy for state '''B''' is also computed. The difference
			between states '''A''' and '''B''' may be in the atom types involved, in which case the ΔG
			obtained is for "mutating" one molecule onto another, or it may be a difference of
			geometry, in which case one obtains a free energy map along one or more [[reaction coordinate]]s.
			This free energy map is also known as a ''[[potential of mean force]]'' or PMF.
			Free energy perturbation calculations only converge properly when the difference
			between the two states is small enough; therefore it is usually necessary to divide a
			perturbation into a series of smaller "windows", which are computed independently.
			Since there is no need for constant communication between the simulation for one
			window and the next, the process can be trivially parallelized by running each window in
			a different CPU, in what is known as an "[[embarrassingly parallel]]" setup.

			FEP calculations have been used for studying host-guest binding energetics,
			[[pKa]] predictions, [[solvent effects]] on reactions, and enzymatic reactions. For the
			study of reactions it is often necessary to involve a [[quantum mechanics\|quantum-mechanical]] representation of
			the reaction center because the [[molecular mechanics]] [[force field (chemistry)\|force field]]s used for FEP simulations can't handle
			breaking bonds. A hybrid method that has the advantages of both QM and MM
			calculations is called [[QM/MM]].

			[[Umbrella sampling]] is another free-energy calculation technique that is typically used for calculating the free-energy change associated with a change in "position" coordinates as opposed to "chemical" coordinates, although Umbrella sampling can also be used for a chemical transformation when the "chemical" coordinate is treated as a dynamic variable (as in the case of the Lambda dynamics approach of Kong and Brooks).
			An alternative to free energy perturbation for computing potentials of mean force in chemical space is [[thermodynamic integration]]. Another alternative, which is probably more efficient, is the [[Bennett acceptance ratio]] method.

			==Software==
			Several software packages have been developed to help perform FEP calculations. Below is a short list of some of the most common programs:
			*[[AMBER]]<ref>http://www.ambermd.org</ref>
			*[[BOSS (molecular mechanics)\|BOSS]]
			*[[CHARMM]]
			*[[Desmond (software)\|Desmond]]
			*[[GROMACS]]
			*[[MacroModel]]
			*[[MOLARIS]]
			*[[NAMD]]
			*[[Tinker]]

			==See also==
			* [[Thermodynamic integration]]
			* [[Umbrella sampling]]

			==References==
			<references />

			[[Category:Computational chemistry]]
			[[Category:Statistical mechanics]]

en>Linas: mention asymptotic equipartition property in main body

2012-07-20T05:02:46Z

mention asymptotic equipartition property in main body

New page

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