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23:10, 21 April 2025 Eew947 talk contribs created page Research:Typer (Copied, haven't checked)
23:09, 21 April 2025 Eew947 talk contribs created page Research:AMOEBA (Copied, haven't checked)
23:08, 21 April 2025 Eew947 talk contribs created page Research:DrugDesign (Copied, haven't checked)
23:07, 21 April 2025 Eew947 talk contribs created page Research:Penetration (Created page with "==Multipoles for monomers== From poltype: ~pren/poltype-1.1.3-dev/poltype.py.0.1 -s *.sdf -n 8 -m 6000MB -M 120GB --do-tor-qm-opt --espbasisset=aug-cc-pvtz & Files are in: ... ==SAPT energy for dimer interactions== ===SAPT2+0 methods=== ===SAPT energy data and structures=== ==CP parameter fitting== ...")
23:07, 21 April 2025 Eew947 talk contribs created page Research:AMOEBA NA (Copied, haven't checked)
23:06, 21 April 2025 Eew947 talk contribs created page Research:Reading (Created page with "=General= '''Molecular Modelling''', Principles and Pllications, Andrew Leach '''Computer simulations of liquids''', Allen & Tildesley '''Molecular Simulations''', Frenkel and Smit =Free energy methods= '''Free energy Calculations''', Theory and Applications in Chemistry and bIology, Chipot and Pophorille, Springer =MD books in dropbox = http://biomol.bme.utexas.edu/wiki/index.php/Software:Tutorials#Modeling_books_in_dropbox https://www.dropbox.com/sh/g3myhes5y1r...")
23:05, 21 April 2025 Eew947 talk contribs created page Research ex:OpenMM (Copied, have not edited. Already see some old links I will have to take care of.)
23:03, 21 April 2025 Eew947 talk contribs created page Research ex:AMOEBA in Amber (Created page with "sander and pmemd modification for ligand binding free enery calculations = Important: read me first = '''Now (as of June 2013) you can use the latest tinker (v6) and parameter files to set up the system in TINKER and then convert for amber run.''' *If you have an spherical ion (e.g. Na+, Cl-, Mg++in the system), you may need to modify the analout (see below) to replace multip...")
23:02, 21 April 2025 Eew947 talk contribs created page Research ex:Tinker OLD (Old version of Tinker tut page with some defunct stuff. Wanted to have it somewhere so it wasn't lost)
22:56, 21 April 2025 Eew947 talk contribs created page Course:blogs (Created page with "== standard formation entropy== *For pure element molecules, the standard formation of free energy and enthalpy are set to 0 (since we only care about relative). *For entropy, however, we use 0K as the reference, so that the absolute entropy of any substance can be measured from Cp vs. T: S(T)=S(0)+integral (Cp/T). *For example, H2 (g)'s standard state absolute entropy (relative to 0K) is 130.6 J/mol K. The standard formation entropy (130.6-130.6) is still 0. The stand...")
22:55, 21 April 2025 Eew947 talk contribs created page Course:ABS (created Course:ABS page. Need to check that files, links, etc are working)
22:54, 21 April 2025 Eew947 talk contribs created page Course: CompMethod (Need to check that courses are somewhere so they can be accessed. All I did to edit here was add the page and change biomole.bme.utexas.edu to biomolmd.org. Don't know if that actually exists)
22:51, 21 April 2025 Eew947 talk contribs created page Research ex:AMOEBA param (added research ex: AMOEBA param) Tag: Visual edit
22:44, 21 April 2025 Eew947 talk contribs moved page Courses: to Category:Courses
22:44, 21 April 2025 Eew947 talk contribs created page Courses: (Created blank page) Tag: Visual edit
22:42, 21 April 2025 Eew947 talk contribs created page CompBiomol (added CompBiomol Course page, need to add Course group category) Tag: Visual edit
22:40, 21 April 2025 Eew947 talk contribs created page Computing Resources & Admin (added computing resources and admin page because I don't think we had it. Have not edited it or anything) Tag: Visual edit
21:34, 10 August 2022 Eew947 talk contribs created page File:Thermocycle2.png
21:34, 10 August 2022 Eew947 talk contribs uploaded File:Thermocycle2.png
21:33, 10 August 2022 Eew947 talk contribs created page File:Thermocycle1.png
21:33, 10 August 2022 Eew947 talk contribs uploaded File:Thermocycle1.png
21:29, 10 August 2022 Eew947 talk contribs created page File:Kd2.png
21:29, 10 August 2022 Eew947 talk contribs uploaded File:Kd2.png
21:02, 10 August 2022 Eew947 talk contribs created page File:Atequil.png
21:02, 10 August 2022 Eew947 talk contribs uploaded File:Atequil.png
20:17, 10 August 2022 Eew947 talk contribs created page File:Freeenergykd.png
20:17, 10 August 2022 Eew947 talk contribs uploaded File:Freeenergykd.png
20:15, 10 August 2022 Eew947 talk contribs created page File:Kdstuff.png
20:15, 10 August 2022 Eew947 talk contribs uploaded File:Kdstuff.png
20:11, 10 August 2022 Eew947 talk contribs created page File:Konoff3.png
20:11, 10 August 2022 Eew947 talk contribs uploaded File:Konoff3.png
20:10, 10 August 2022 Eew947 talk contribs created page File:Konoff2.png
20:10, 10 August 2022 Eew947 talk contribs uploaded File:Konoff2.png
20:09, 10 August 2022 Eew947 talk contribs created page File:Konoff.png
20:09, 10 August 2022 Eew947 talk contribs uploaded File:Konoff.png
20:06, 10 August 2022 Eew947 talk contribs created page File:5maf in17.png
20:06, 10 August 2022 Eew947 talk contribs uploaded File:5maf in17.png
20:03, 10 August 2022 Eew947 talk contribs created page File:Lanmodulin.png
20:03, 10 August 2022 Eew947 talk contribs uploaded File:Lanmodulin.png
20:01, 10 August 2022 Eew947 talk contribs created page File:5maf in17 fancylumps2.png
20:01, 10 August 2022 Eew947 talk contribs uploaded File:5maf in17 fancylumps2.png
19:58, 10 August 2022 Eew947 talk contribs created page File:AMOEBAeqs.png
19:58, 10 August 2022 Eew947 talk contribs uploaded File:AMOEBAeqs.png
19:56, 10 August 2022 Eew947 talk contribs created page File:Zwanzig EQ.png
19:56, 10 August 2022 Eew947 talk contribs uploaded File:Zwanzig EQ.png
19:54, 10 August 2022 Eew947 talk contribs created page File:Bfe1.png
19:54, 10 August 2022 Eew947 talk contribs uploaded File:Bfe1.png
19:52, 10 August 2022 Eew947 talk contribs created page File:BFE Energy-vs-RC.png
19:52, 10 August 2022 Eew947 talk contribs uploaded File:BFE Energy-vs-RC.png
13:31, 9 August 2022 Eew947 talk contribs created page Ammm:ProteinLigandBFE (Created page with "= Protein-Ligand Binding Free Energy (Elizabeth E. Wait) = == Introduction == Small Difference Between Large Numbers == Why might we care about getting binding free energy == blah == What is binding free energy (what does it actually mean, esp. protein-ligand) == blah == How do we get it == Force Fields Intro AMOEBA is cool BAR - Justin talking about later Restraints Previous Results - Chemical Accuracy == Things to Think About == Entropy Enthalpy Induced Fit...") Tag: Visual edit

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