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2026-08-14T19:10:39Z
User contributions
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https://biomolmd.org/mw/index.php?title=Tutorial:amm&diff=1734
Tutorial:amm
2022-05-26T17:52:10Z
<p>Bdw2: </p>
<hr />
<div>'''Advanced Molecular Modeling Methods''' <br />
<br />
<br />
<br />
= ''Molecular Mechanics and Force Fields (Ren, 3 lectures)'' =<br />
<br />
== [[ammm:Mm_gff|Molecular Mechanics and General force fields]] ==<br />
<br />
== [[ammm:Mm_mpole|Electrostatic:polarizable multipole]] ==<br />
<br />
== [[ammm:Mm_ewald|Ewald and vdw long range correction]] ==<br />
<br />
== [[ammm:Mm_aplus|AMOEBA+]] ==<br />
<br />
= ''Molecular Dynamics'' =<br />
<br />
== [[ammm:Md_ham|Lagrangian and Hamiltonian]] (Ren) ==<br />
<br />
== [[ammm:Md_erg|Liouville Equation and Ergodicity]] ==<br />
<br />
== [[ammm:Md_integrator|Integrator and constrain]] ==<br />
<br />
== [[ammm:Md_tp|Temperature and Pressure control]] ==<br />
<br />
== [[ammm:stoch |Stochastic/Langevin/Brownian/DPD dynamics]] ==<br />
<br />
= ''Deriving force field parameters for a new molecule/unit'' =<br />
<br />
== [[ammm:Ff_gau_grom_prdrug|Gaussian and gromacs and prodrug server (Fonner)]] ==<br />
<br />
== [[ammm:Ff_amber_ligand_parameter|Amber and Antechamber (Chunli)]]==<br />
<br />
== [[ammm:Lig_ion_params|Metal ion and ligand parameterizations (Oscar) 9/30]] ==<br />
<br />
= [[ammm:QM/MM|QM/MM (Chistina)]] =<br />
<br />
= [[Ammm:Poltype 2|Poltype 2 - Small molecule parameter derivation]] =<br />
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= ''Implicit Solvent approach'' =<br />
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== [[ammm:Gb_gk|GB/GK (Jenny 10/12)]] ==<br />
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== [[ammm:PB_(APBS)|PB (APBS)(Yue)]] ==<br />
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== [[ammm:Molecular_surfaces|Calculation of molecular surface (Maysam)]] <span style="background-color: rgb(255, 102, 0);">10/19</span> ==<br />
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== [[ammm:Nonpolar_solvation|Nonpolar Solvation and hydrophobicity (Jenny 10/21)]] ==<br />
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= ''Sampling'' =<br />
<br />
== [[ammm:Free_energy_simulations|Free energy simulations]] (Johnny) ==<br />
<br />
== [[ammm:Umbrella_sampling_and_WHAM|Umbrella sampling and WHAM]] (Yue) <span style="background-color: rgb(255, 102, 0);">10/28</span> ==<br />
<br />
== [[ammm:REMD_jenny|REMD with gromacs (Jenny)]] ==<br />
<br />
== [[ammm:Adaptive_umbrella_sampling|Multicanonical and adaptive umbrella sampling]] (Bruce) <span style="background-color: rgb(255, 102, 0);">11/4</span> ==<br />
<br />
== [[Non_equilibrium_method_and_AFM_simulation_w_gromacs|Non equilibrium method and AFM simulation w gromacs]] (Tim) <span style="color: rgb(255, 102, 0);">11/11(out of town on 11/9)</span> ==<br />
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= ''Protein-ligand binding'' =<br />
<br />
== [[ammm:Flexible_Docking_with_GOLD_and_GLIDE|Docking (Glide and gold) and flexibility (Maysam)]] <span style="background-color: rgb(255, 102, 0);">11/16</span> ==<br />
<br />
== [[ammm:MM/PBSA_with_amber:_theory_and_application|MM/PBSA with amber: theory and application]](chunli) <span style="background-color: rgb(255, 102, 0);">11/18</span> ==<br />
<br />
== FEP/BAR, TI (Oscar) cancelled ==<br />
see <br />
* [[ammm:Free_energy_simulations|Free energy simulations (Johnny)]]<br />
* http://alchemistry.org/wiki/Main_Page<br />
<br />
Free Energy Perturbation<br />
BAR<br />
Thermodynamic Integration<br />
Metadynamics<br />
Orthogonal Space Random Walk<br />
<br />
Read books:<br />
<br />
*Molecular Modeling by Andrew Leach<br />
*Free energy calculations (Chipot et al )<br />
*And papers by Ren lab.<br />
<br />
= Electrostatics =<br />
<br />
== [[ammm:Comparative_Analysis_of_RNA_And_Mfold|Comparative Analysis of RNA And Mfold]] (David) <span style="background-color: rgb(255, 102, 0);">11/25</span> ==<br />
<br />
= ''Coarse-grained modeling'' =<br />
<br />
== [[ammm:Coarse_grain_modeling|Gay-Berne and coarse-grain modeling (Johnny) 11/30]] ==<br />
<br />
== [[ammm:Rigid_body_MD_(Steven_12/2) | Rigidbody mechanics]] ==<br />
<br />
<br />
<br />
== Psudo atom RNA model (Bruce) canceled ==<br />
<br />
= ''Reaction Path and TST'' =<br />
<br />
== Reaction path search (David) canceled ==<br />
<br />
== Nudged Elastic Band (NEB) in AMBER (Oscar) canceled ==<br />
<br />
[http://ambermd.org/tutorials/advanced/tutorial5/index.htm http://ambermd.org/tutorials/advanced/tutorial5/index.htm]<br />
<br />
[http://www.quantumwise.com/documents/manuals/ATK-2008.10/chap.relax.html#chap.relax.neb.intro http://www.quantumwise.com/documents/manuals/ATK-2008.10/chap.relax.html#chap.relax.neb.intro]<br />
<br />
= Continuum method for biomolecules (Steven) canceled or merged with above =<br />
<br />
*Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods <br />
<br />
Mar 21, 2005 Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J, 88, 1659-1666, 2005.<br />
<br />
*Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis <br />
<br />
Sep 1, 2004 Song Y, Zhang Y, Bajaj C, Baker NA. Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis. Biophys J, 87, 1558-1566, 2004.<br />
<br />
*Finite element solution of the steady-state Smoluchowksi equation for rate constant calculations <br />
<br />
Apr 1, 2004 Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA. Finite element solution of the steady-state Smoluchowksi equation for rate constant calculations. Biophys J, 86, 2017-2029, 2004.<br />
<br />
*Finite element simulations of acetylcholine diffusion in neuromuscular junctions <br />
<br />
Dec 12, 2002 Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J, 84, 2234-2241, 2003.<br />
<br />
= Online Resource =<br />
<br />
== Gromacs tutorial ==<br />
<br />
[http://www.dddc.ac.cn/embo04/#Practicals http://www.dddc.ac.cn/embo04/#Practicals]<br />
<br />
== AMBER tutorial ==<br />
<br />
[http://ambermd.org/tutorial/ http://ambermd.org/tutorial/]<br />
<br />
[http://ambermd.org/tutorials/ http://ambermd.org/tutorials/]</div>
Bdw2
https://biomolmd.org/mw/index.php?title=Ammm:Poltype_2&diff=1733
Ammm:Poltype 2
2022-05-26T17:51:46Z
<p>Bdw2: </p>
<hr />
<div>[[File:Poltype2.pdf|thumb]]</div>
Bdw2
https://biomolmd.org/mw/index.php?title=Ammm:Poltype_2&diff=1732
Ammm:Poltype 2
2022-05-26T17:50:57Z
<p>Bdw2: </p>
<hr />
<div>[[File:Poltype2.pdf|thumb]]<br />
Testing</div>
Bdw2
https://biomolmd.org/mw/index.php?title=File:Poltype2.pdf&diff=1731
File:Poltype2.pdf
2022-05-26T17:50:37Z
<p>Bdw2: </p>
<hr />
<div>Presentation</div>
Bdw2
https://biomolmd.org/mw/index.php?title=Ammm:Poltype_2&diff=1730
Ammm:Poltype 2
2022-05-26T17:49:30Z
<p>Bdw2: Created page with "Testing"</p>
<hr />
<div>Testing</div>
Bdw2