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- 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
- ...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 simula2 KB (261 words) - 14:20, 21 May 2012
- ..., 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
- ...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 quick8 KB (1,255 words) - 21:36, 10 July 2013
- ...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
- #REDIRECT [[Free Energy Fundamentals]]38 bytes (4 words) - 21:24, 14 February 2013
- ...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 cut2 KB (278 words) - 13:18, 27 September 2013
- 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 expand10 KB (1,578 words) - 18:36, 18 June 2013
- 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.beva21 KB (3,498 words) - 03:31, 4 April 2018
- = 2010 Workshop on Free Energy Methods in Drug Design = Since their first application decades ago, free energy methods have17 KB (2,402 words) - 09:47, 20 May 2010
- #REDIRECT [[GROMACS 4.6 example: Direct ethanol solvation free energy]]71 bytes (8 words) - 21:28, 15 April 2013
- ...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
- = 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 par18 KB (2,506 words) - 21:22, 21 May 2012
- 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 par28 KB (3,899 words) - 13:07, 16 June 2014
- ...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 - how24 KB (3,198 words) - 02:28, 23 May 2023
- Free Energy Methods ...e written by hand. Registration: https://cbd.eventsair.com/alchemical-free-energy-workshop-2024/registration/Site/Register9 KB (1,289 words) - 08:59, 16 May 2024
- | 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 alternate50 KB (7,055 words) - 13:17, 20 June 2021
- #REDIRECT [[2016 Workshop on Free Energy Methods in Drug Design: Targeting Cancer]]83 bytes (11 words) - 13:28, 23 October 2015
- ...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 a12 KB (1,617 words) - 02:27, 20 September 2022
- 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 par23 KB (3,155 words) - 18:42, 8 October 2019
- 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 par32 KB (4,607 words) - 15:32, 3 July 2018
Page text matches
- * '''[[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
- 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
- ...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
- ...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
- ...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
- ...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
- {{Free Energy Howto}} Included below are a number of free energy tutorials for a variety of molecular programs. They do not necessarily all3 KB (377 words) - 07:29, 23 March 2017
- 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
- ..., 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
- ...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
- === <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 between1 KB (176 words) - 08:26, 5 July 2011
- ...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 that1 KB (143 words) - 13:32, 18 October 2007
- ...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
- ...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 cut2 KB (278 words) - 13:18, 27 September 2013
- ...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
- #REDIRECT [[Free Energy Fundamentals]]38 bytes (4 words) - 12:15, 27 February 2013
- #REDIRECT [[Free Energy Fundamentals]]38 bytes (4 words) - 12:11, 27 February 2013
- #REDIRECT [[2014 Workshop on Free Energy Methods in Drug Design]]65 bytes (9 words) - 07:46, 19 May 2014
- #REDIRECT [[2016 Workshop on Free Energy Methods in Drug Design: Targeting Cancer]]83 bytes (11 words) - 13:28, 23 October 2015
- ...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) - 11:37, 15 May 2016
- ...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
- ...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 ''d1 KB (196 words) - 19:11, 9 October 2007
- ...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 int1 KB (245 words) - 12:21, 23 October 2007
- ...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 simula2 KB (261 words) - 14:20, 21 May 2012
- [[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 avoided5 KB (782 words) - 04:11, 19 September 2019
- [[Category:Binding Free Energy Calculations]]404 bytes (48 words) - 16:30, 18 October 2007
- 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
- ...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 quick8 KB (1,255 words) - 21:36, 10 July 2013
- ...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 literatur426 bytes (67 words) - 14:16, 18 June 2013
- ...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 th7 KB (1,146 words) - 16:32, 19 March 2015
- ...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
- ...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
- ...mmon constants and variables that are seen throughout the [[:Category:Free Energy Fundamentals|fundamentals sections.]] Although the Table itself is not in a | Potential Energy8 KB (1,290 words) - 12:44, 8 July 2013
- 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
- [[Category:Free Energy Reviews]]704 bytes (96 words) - 15:45, 18 October 2007
- What is the current state of free energy calculations in drug design When queried, pretty much all industry attendees have run some free energy calculations6 KB (977 words) - 11:18, 5 June 2014
- ...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
- ''What is the current state of free energy calculations in drug design?'' Pretty much all industry attendees have run some free energy calculations6 KB (972 words) - 08:04, 27 May 2014
- [[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 metho8 KB (1,351 words) - 16:53, 18 June 2013
- ...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
- ...simulation software should I use?" So long as the software can handle free energy calculations (or you can make it), and collects the information the analysi ...ed. Many simulation software packages actually run or recommend you run an energy minimization step prior to beginning to correct for possible overlapping mo13 KB (2,018 words) - 08:35, 13 July 2013
- ...ed in the theory section of these fundamentals talks about how you get the free energies, but will also be recapped here. This page also talks about how yo =Calculating Free Energies=9 KB (1,451 words) - 18:25, 18 June 2013
- 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 expand10 KB (1,578 words) - 18:36, 18 June 2013
- ...blem with three or four codes. e.g. let's compute a specific binding free energy Matteo: Put up T4 lysozyme example for absolute binding free energies (on alchemistry.org)4 KB (599 words) - 13:55, 26 May 2014
- ...w a tutorial here for [[GROMACS 4.6 example: Direct ethanol solvation free energy|the standard way to perform the simulation]]. The topology and gro files ...e states defined to perform the calculation of the absolute solvation free energy of ethanol (also known as the11 KB (1,266 words) - 12:17, 23 May 2014
- AMBER/CHARMM compute things like kinetic energy differently, so may be challenges in comparing should have guidelines for validating/evaluating new free energy codes6 KB (977 words) - 13:47, 26 May 2014
- Tuesday Afternoon Discussion: Making free energy calculations robust. ** We have databases of chemical reactions, why cant we have then for Free Energy transformations?5 KB (893 words) - 13:22, 26 May 2014
- ...ot go deeply into all these methods. They are not needed to carry out free energy calculations, but they may be extremely useful to converge calculations in ...finities (e.g. different torsional states). Doing this allows for the free energy components to be properly computed and then combined.{{cite|Wang2006}}{{cit16 KB (2,261 words) - 17:09, 21 February 2015
- ...will be different still from the other [[Example: Absolute Solvation Free Energy|two]] [[Example: Relative Binding Affinity|examples]] in that this will tou For this particular example, we will look at the absolute binding free energies of toluene in the apolar cavity of T4 Lysozyme. Furthermore, since18 KB (2,834 words) - 18:39, 18 June 2013
- ...binding site in a different simulated system. In both cases, the computed free energies can depend on details of the calculation setup, such as the bounda ...to remove these free energy contributions before comparing simulated free energy results with experimental results.13 KB (2,068 words) - 20:27, 4 July 2014