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  • Free Energy References
    This is a list of free energy categories. Select the category, and add any references. You will need to [[:Category:Free Energy Reviews]]
    686 bytes (103 words) - 23:25, 28 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) - 13:20, 21 May 2012
  • Free Energy Applications
    ..., and Roland Kjellander. "In Silico Prediction of Drug Solubility: 1. Free Energy of Hydration". J. Phys. Chem. B. ASAP article (2007). [http://dx.doi.org/10 ..., and Roland Kjellander. "In Silico Prediction of Drug Solubility: 2. Free Energy of Solvation in Pure Melts". J. Phys. Chem. B. ASAP article (2007). [http:/
    961 bytes (132 words) - 21:24, 17 October 2007
  • 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) - 20:36, 10 July 2013
  • Example Free Energy Calculations
    ...Virginia Tech available if you would like specific instructions for a free energy simulation. ...sult any of the examples below to see how to go about setting up your free energy calculation:
    2 KB (319 words) - 06:33, 26 September 2016
  • Free Energy Introduction
    #REDIRECT [[Free Energy Fundamentals]]
    38 bytes (4 words) - 20:24, 14 February 2013
  • Free energy results
    ...mation used to calculate the free energy of binding. Unlike the potential energy results, the goal should be a free energy that is independent of _all_ possible nonphysical parameters (vdW/Ewald cut
    2 KB (278 words) - 12:18, 27 September 2013
  • Example: Absolute Solvation Free Energy
    This page will guide you through the process of designing a simple free energy simulation. In particular, this example will set up an OPLS-AA forcefield s ...ions on how to run this calculation with GROMACS 4.6]] using standard free energy calculations, or using [[GROMACS 4.6 example: Ethanol solvation with expand
    10 KB (1,578 words) - 17:36, 18 June 2013
  • Absolute Binding Free Energy - Gromacs 2016
    In this tutorial we will calculate the free energy of binding (<math>\Delta G^{o}_{b}</math> ; i.e. affinity) of a ligand for ...ggested to go through [[GROMACS 4.6 example: Direct ethanol solvation free energy|>this<]] ethanol solvation tutorial on alchemistry.org, or [http://www.beva
    21 KB (3,498 words) - 02:31, 4 April 2018
  • 2010 Workshop on Free Energy Methods in Drug Design
    = 2010 Workshop on Free Energy Methods in Drug Design = Since their first application decades ago, free energy methods have
    17 KB (2,402 words) - 08:47, 20 May 2010
  • Gromacs 4.6 example: Direct ethanol solvation free energy
    #REDIRECT [[GROMACS 4.6 example: Direct ethanol solvation free energy]]
    71 bytes (8 words) - 20:28, 15 April 2013
  • GROMACS 4.6 example: Direct ethanol solvation free energy
    ...e states defined to perform the calculation of the absolute solvation free energy of ethanol (also known as the ...es]] alchemical-gromacs.py will be in the pymbar-examples/alchemical-free-energy directory. Go to the web page and 'git clone' the files:
    13 KB (1,770 words) - 19:59, 5 June 2014
  • 2012 Workshop on Free Energy Methods in Drug Design
    = 2012 Workshop on Free Energy Methods in Drug Design = ...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
    18 KB (2,506 words) - 20:22, 21 May 2012
  • 2014 Workshop on Free Energy Methods in Drug Design
    The 2014 Workshop on the State of Free Energy Calculations in Drug Design<br> ...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
    28 KB (3,899 words) - 12:07, 16 June 2014
  • 2023 Workshop on Free Energy Methods in Drug Design
    ...from the schedule 2020 event, and will focus on the current state of free energy techniques. Registration for the 2020 conference will be held. Refunds are As this is the 10(+3)th birthday of the first 2010 free energy workshop, we will be holding a session celebrating the last 10 years - how
    24 KB (3,198 words) - 01:28, 23 May 2023
  • 2024 Workshop on Free Energy Methods in Drug Design
    Free Energy Methods ...e written by hand. Registration: https://cbd.eventsair.com/alchemical-free-energy-workshop-2024/registration/Site/Register
    9 KB (1,310 words) - 03:46, 31 May 2024
  • 2020 Workshop on Free Energy Methods in Drug Design
    | Julien Michel (Edinburgh) - Adaptive absolute binding free energy calculations for lead compounds and flexible proteins ''recorded'' | Hannah Baumann (UC Irvine, Mobley lab) - Binding free energy calculations: Sampling challenges, nonequilibrium switching, and alternate
    50 KB (7,055 words) - 12:17, 20 June 2021
  • 2016 Summit and Workshop on Free Energy Methods in Drug Design
    #REDIRECT [[2016 Workshop on Free Energy Methods in Drug Design: Targeting Cancer]]
    83 bytes (11 words) - 12:28, 23 October 2015
  • 2022 Virtual Workshop on Free Energy Methods in Drug Design
    ...Free Energy Meeting to be held in May 2023, we are hosting a virtual free energy meeting to give an opportunity to early career researchers* to present thei Registration is free and open! Spaces are many but finite, please only register with one email a
    12 KB (1,617 words) - 01:27, 20 September 2022
  • 2016 Workshop on Free Energy Methods in Drug Design: Targeting Cancer
    The 2016 Workshop on Free Energy Calculations in Drug Design: Targeting Cancer <br> ...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
    23 KB (3,155 words) - 17:42, 8 October 2019

Page text matches

  • Events
    * '''[[2024 Workshop on Free Energy Methods in Drug Design]]''' * '''[[2023 Workshop on Free Energy Methods in Drug Design]]'''
    859 bytes (129 words) - 10:05, 3 July 2023
  • Free Energy References
    This is a list of free energy categories. Select the category, and add any references. You will need to [[:Category:Free Energy Reviews]]
    686 bytes (103 words) - 23:25, 28 October 2007
  • JChangJPhysChemB2007a
    ...on Chang, Abraham Lenhoff, and Stanley I. Sandler | title = Solvation free energy of amino acids and side-chain analogues | journal = J. Phys. Chem. B. | vol [[Category: Solvation Free Energy Calculations]]
    320 bytes (40 words) - 17:02, 18 October 2007
  • JWestergrenJPhysChemB2007a
    ...land Kjellander | title = In Silico Prediction of Drug Solubility: 1. Free Energy of Hydration | journal = J. Phys. Chem. B.| volume = ASAP article | year = [[Category:Solvation Free Energy Calculations]]
    379 bytes (49 words) - 17:05, 18 October 2007
  • KLuderJPhysChemB2007a
    ...land Kjellander | title = In Silico Prediction of Drug Solubility: 2. Free Energy of Solvation in Pure Melts | journal = J. Phys. Chem. B.| volume = ASAP art [[Category:Solvation Free Energy Calculations]]
    369 bytes (49 words) - 17:06, 18 October 2007
  • DLMobleyJChemPhys2006a
    ...se of orientational restraints and symmetry corrections in alchemical free energy calculations | journal = J. Chem. Phys. | volume = 125 | pages = 084902 | [[Category:Binding Free Energy Calculations]]
    400 bytes (48 words) - 17:09, 18 October 2007
  • Tutorials
    {{Free Energy Howto}} Included below are a number of free energy tutorials for a variety of molecular programs. They do not necessarily all
    3 KB (377 words) - 06:29, 23 March 2017
  • GJayachandranJChemPhys2006a
    title = Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics| [[Category:Binding Free Energy Calculations]]
    417 bytes (45 words) - 13:05, 18 October 2007
  • Free Energy Applications
    ..., and Roland Kjellander. "In Silico Prediction of Drug Solubility: 1. Free Energy of Hydration". J. Phys. Chem. B. ASAP article (2007). [http://dx.doi.org/10 ..., and Roland Kjellander. "In Silico Prediction of Drug Solubility: 2. Free Energy of Solvation in Pure Melts". J. Phys. Chem. B. ASAP article (2007). [http:/
    961 bytes (132 words) - 21:24, 17 October 2007
  • CChipotJComputAidMolDes2005a
    ...Christophe Chipot, Xavier Rozanska, and Surjit B. Dixit | title = Can free energy calculations be fast and accurate at the same time? Binding of low-affinity [[Category:Binding Free Energy Calculations]]
    460 bytes (61 words) - 12:35, 18 October 2007
  • Tutorial Gromacs 4 5 3
    === <font size="+2" color="0000FF">Free Energy Calculations: Methane in Water</font> === ...orial will guide the user through the process of calculating a simple free energy change, the decoupling (i.e. removal) of van der Waals interactions between
    1 KB (176 words) - 07:26, 5 July 2011
  • TRodingerCurrOpinStructBio2005a
    ...mes | title = Enhancing the accuracy, the efficiency and the scope of free energy simulations | journal = Curr. Opin. Struct. Bio. | year = 2005 | volume = Groups free energy methods into three classes: FEP and other non-equilibrium work methods that
    1 KB (143 words) - 12:32, 18 October 2007
  • About the Editors
    ...a.edu The University of Virginia]. He has done a number of studies on free energy methods and calculation: see [https://www.colorado.edu/chbe/michael-r-shirt ...up/people.php#grads in the Shirts Group]. Background in computational free energy software development and currently CMS software development and training.
    1 KB (209 words) - 12:06, 24 February 2020
  • Free energy results
    ...mation used to calculate the free energy of binding. Unlike the potential energy results, the goal should be a free energy that is independent of _all_ possible nonphysical parameters (vdW/Ewald cut
    2 KB (278 words) - 12:18, 27 September 2013
  • Example Free Energy Calculations
    ...Virginia Tech available if you would like specific instructions for a free energy simulation. ...sult any of the examples below to see how to go about setting up your free energy calculation:
    2 KB (319 words) - 06:33, 26 September 2016
  • Theoretic Principals
    #REDIRECT [[Free Energy Fundamentals]]
    38 bytes (4 words) - 11:15, 27 February 2013
  • Theoretic Principles
    #REDIRECT [[Free Energy Fundamentals]]
    38 bytes (4 words) - 11:11, 27 February 2013
  • 2014WFEDD
    #REDIRECT [[2014 Workshop on Free Energy Methods in Drug Design]]
    65 bytes (9 words) - 06:46, 19 May 2014
  • 2016 Summit and Workshop on Free Energy Methods in Drug Design
    #REDIRECT [[2016 Workshop on Free Energy Methods in Drug Design: Targeting Cancer]]
    83 bytes (11 words) - 12:28, 23 October 2015
  • Main Page
    ...pproach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving =Getting Started with Free Energy Methods=
    7 KB (965 words) - 10:37, 15 May 2016

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