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• 2018 Workshop on Free Energy Methods, Kinetics and Markov State Models in Drug Design
  This first three days of the this workshop focus on free energy techniques—the latest innovations and use cases, force field paramete ...ay and what challenges must be tackled next to bring the potential of free energy techniques to bear on real-world applications. We also seek to identify par
  32 KB (4,607 words) - 15:32, 3 July 2018

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• PWFowlerPhilTransRSocA2005a
  ...d steered thermodynamic integration accelerates the calculation of binding free energies | journal = Phil. Trans. R. Soc. A | year = 2005 | volume = 363 [[Category:Binding Free Energy Calculations]]
  415 bytes (47 words) - 18:10, 18 October 2007
• Decoupling and annihilation
  ...and ''annihilation'' have been used in somewhat confusing ways in the free energy literature, so we want to clarify the definitions we use. In our terminolog ...'' to refer to whether or not restraints are used in absolute binding free energy calculations. In our view this is confusing, since ''annihilation'' and ''d
  1 KB (196 words) - 19:11, 9 October 2007
• Why Alchemistry.org?
  ...ting up alchemistry.org is to provide an accessible point of entry to free energy calculations. Ultimately, we want these pages to provide both a concise int
  1 KB (245 words) - 12:21, 23 October 2007
• Free Energy Tools
  ...rientational restraints and symmetry number corrections in alchemical free energy calculations", Journal of Chemical Physics 125:084902, 2006. ...inty estimates are available. This can be used to analyze alchemical free energy calculations, umbrella sampling simulations, or generalized-ensemble simula
  2 KB (261 words) - 14:20, 21 May 2012
• Exponential Averaging
  [[Category:Free Energy Fundamentals]] ...named after the person who first derived it){{Cite|Zwanzig1954}} and "free energy perturbation (FEP)." To avoid confusion, the latter term should be avoided
  5 KB (782 words) - 04:11, 19 September 2019
• BZagrovicJChemTheoryComput2007a
  [[Category:Binding Free Energy Calculations]]
  404 bytes (48 words) - 16:30, 18 October 2007
• Thermodynamic Cycle
  In any free energy calculation, one must decide on what thermodynamic cycle they will define a ...|300px|Three simple molecules that could serve as your end states for free energy differences]]
  5 KB (808 words) - 13:18, 7 January 2013
• Free Energy Fundamentals
  ...seen throughout the rest of the [[:Category:Free Energy Fundamentals|free energy fundamentals]] pages and in the literature as a whole. ...repository of the background mathematics and principals required for free energy calculations, but it will serve as a good start point and hopefully a quick
  8 KB (1,255 words) - 21:36, 10 July 2013
• How You Can Help
  ...r these pages to provide an up-to-date introduction to how to perform free energy calculations, including citations to the latest and most relevant literatur
  426 bytes (67 words) - 14:16, 18 June 2013
• Bennett Acceptance Ratio
  ...r, ''requires configuration information from two states'' to estimate free energy differences. ...optimal way to use the information between two states, improving the free energy estimate. This is where Bennett started his derivation and, since he was th
  7 KB (1,146 words) - 16:32, 19 March 2015
• Test System Repository
  ...complexity for use by the free energy simulation community. Note that the free energies provided by these systems may not agree particularly well with exp * [[Potential energy results]]
  6 KB (935 words) - 10:55, 10 August 2016
• The Simple Molecular Benchmark Test Set
  ...ormation is performed, but allows these systems to be used to improve free energy pathways as well. * System: Simplest molecular free energy system = UA methane in TIP3P water.
  4 KB (544 words) - 21:29, 10 July 2013
• Definitions
  ...mmon constants and variables that are seen throughout the [[:Category:Free Energy Fundamentals|fundamentals sections.]] Although the Table itself is not in a | Potential Energy
  8 KB (1,290 words) - 12:44, 8 July 2013
• The Simple Small Molecule Solvation Benchmark Test Set
  This test set was designed to be cheap enough to compare free energy methods, yet difficult enough to provide a challenge. * System: Simplest molecular free energy system = UA methane in TIP3P water.
  3 KB (496 words) - 22:46, 23 September 2013
• MKGilsonAnnuRevBiophysBiomolStruct2007a
  [[Category:Free Energy Reviews]]
  704 bytes (96 words) - 15:45, 18 October 2007
• 2014 Workshop Monday Lunchtime Discussion
  What is the current state of free energy calculations in drug design When queried, pretty much all industry attendees have run some free energy calculations
  6 KB (977 words) - 11:18, 5 June 2014
• Multistate Bennett Acceptance Ratio
  ...o BAR in the limit that only two states are sampled. This equation of free energy calculations can also be seen as a zero-width bin [[Weighted Histogram Anal Much like WHAM, the free energies provided by this method are only a statistical estimator, however,
  7 KB (1,309 words) - 15:40, 10 June 2018
• Monday Lunchtime Discussion
  ''What is the current state of free energy calculations in drug design?'' Pretty much all industry attendees have run some free energy calculations
  6 KB (972 words) - 08:04, 27 May 2014
• Thermodynamic Integration
  [[Category:Free Energy Fundamentals]] ...basic relationship can be calculated by taking the derivative of the free energy difference with respect to <math>\lambda</math>. It is one of the few metho
  8 KB (1,351 words) - 16:53, 18 June 2013
• Weighted Histogram Analysis Method
  ...th is the alchemical variable. From these probabilities, you can calculate free energies and other observables. ...t. Consider the [[Theoretic Principals#Core Free Energy Equation|core free energy difference]] equation between two states <math>i</math> and <math>j</math>
  9 KB (1,549 words) - 11:21, 17 July 2013

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