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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) - 00:25, 29 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
  • 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) - 22:24, 17 October 2007
  • Category:Free Energy Applications
    1 member (0 subcategories, 0 files) - 22:25, 17 October 2007
  • Category:Free Energy Reviews
    A number of reviews of free energy methods and applications
    2 members (0 subcategories, 0 files) - 15:46, 18 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) - 21:36, 10 July 2013
  • Category:Free Energy Fundamentals
    This category is where the fundamentals of free energy calculations are all grouped together.
    22 members (0 subcategories, 0 files) - 11:03, 18 September 2012
  • 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) - 07:33, 26 September 2016
  • Free Energy Introduction
    #REDIRECT [[Free Energy Fundamentals]]
    38 bytes (4 words) - 21:24, 14 February 2013
  • Template:Free Energy Howto
    | name = Free Energy Howto | title = Free Energy How-to's
    1 KB (143 words) - 07:32, 23 March 2017
  • 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) - 13:18, 27 September 2013
  • Talk:Free Energy Fundamentals
    === Free energy difference equation === ...contain only the positions, since the momenta cancel each other out in the free difference equation. Therefore, the phase spaces become configuration space
    663 bytes (110 words) - 00:49, 6 April 2016
  • Category:Solvation Free Energy Calculations
    Papers which deal primarily with determining solvation free energies.
    3 members (0 subcategories, 0 files) - 10:46, 18 October 2007
  • Category:Binding Free Energy Calculations
    ...rily concerned with calculating the binding free energy of ligands by free energy methods.
    5 members (0 subcategories, 0 files) - 10:53, 18 October 2007
  • 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) - 18:36, 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) - 03:31, 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) - 09:47, 20 May 2010
  • Talk:2010 Workshop on Free Energy Methods in Drug Design
    * Christopher Bayly (Merck Frosst) - ''Trying to Avoid Free Energy Calculations using MMPBSA'' * Matt Clark (Pharmatrope) - ''Fast free energy calculation based on Monte Carlo sampling of pose and conformation with a f
    33 KB (4,836 words) - 11:56, 11 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) - 21:28, 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) - 20:59, 5 June 2014

Page text matches

  • Template:Free Energy Howto
    | name = Free Energy Howto | title = Free Energy How-to's
    1 KB (143 words) - 07:32, 23 March 2017
  • Events
    * '''[[2024 Workshop on Free Energy Methods in Drug Design]]''' * '''[[2023 Workshop on Free Energy Methods in Drug Design]]'''
    859 bytes (129 words) - 11:05, 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) - 00:25, 29 October 2007
  • Category:Binding Free Energy Calculations
    ...rily concerned with calculating the binding free energy of ligands by free energy methods.
    5 members (0 subcategories, 0 files) - 10:53, 18 October 2007
  • File:Energy comparisons.tgz
    Energy comparisons for the benchmark test set for free energy calculations.
    (194 KB) - 10:36, 28 August 2011
  • MediaWiki:Sidebar
    ** Free Energy Fundamentals|Free Energy Fundamentals ** http://www.citeulike.org/groupfunc/14929/home | Free Energy References (external)
    449 bytes (46 words) - 18:10, 11 July 2013
  • 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) - 18:02, 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) - 18:05, 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) - 18:06, 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) - 18:09, 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) - 07:29, 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) - 14:05, 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) - 22:24, 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) - 13:35, 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) - 08:26, 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) - 13:32, 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) - 13:06, 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) - 13:18, 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) - 07:33, 26 September 2016
  • Category:Application
    Applications of free energy calculations
    0 members (0 subcategories, 0 files) - 11:14, 18 October 2007

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