Tutorials:amm: Difference between revisions
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Created page with "'''Advanced Molecular Modeling Methods''' = ''Molecular Mechanics and Force Fields (Ren, 3 lectures)'' = == Molecular Mechanics and General force fields == == Electrostatic:polarizable multipole == == Ewald and vdw long range correction == == AMOEBA+ == = ''MD (Ren, 4 lectures)'' = == Lagrangian and Hamiltonian (Ren) == == Liouville Equation and Ergodicity ==..." |
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== [[ammm:Mm_aplus|AMOEBA+]] == | == [[ammm:Mm_aplus|AMOEBA+]] == | ||
= '' | = ''Molecular Dynamics'' = | ||
== [[ammm:Md_ham|Lagrangian and Hamiltonian]] (Ren) == | == [[ammm:Md_ham|Lagrangian and Hamiltonian]] (Ren) == | ||
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== [[ammm:Md_tp|Temperature and Pressure control]] == | == [[ammm:Md_tp|Temperature and Pressure control]] == | ||
== Stochastic/Langevin/Brownian/DPD | == [[ammm:stoch |Stochastic/Langevin/Brownian/DPD dynamics]] == | ||
= ''Deriving force field parameters for a new molecule/unit'' = | = ''Deriving force field parameters for a new molecule/unit'' = | ||
| Line 49: | Line 47: | ||
= ''Sampling'' = | = ''Sampling'' = | ||
== [[ammm:Free_energy_simulations|Free energy simulations]] (Johnny) | == [[ammm:Free_energy_simulations|Free energy simulations]] (Johnny) == | ||
== [[ammm:Umbrella_sampling_and_WHAM|Umbrella sampling and WHAM]] (Yue) <span style="background-color: rgb(255, 102, 0);">10/28</span> == | == [[ammm:Umbrella_sampling_and_WHAM|Umbrella sampling and WHAM]] (Yue) <span style="background-color: rgb(255, 102, 0);">10/28</span> == | ||
== [[ammm:REMD_jenny|REMD with gromacs (Jenny)]] == | == [[ammm:REMD_jenny|REMD with gromacs (Jenny)]] == | ||
== [[ammm:Adaptive_umbrella_sampling|Multicanonical and adaptive umbrella sampling]] (Bruce) <span style="background-color: rgb(255, 102, 0);">11/4</span> == | == [[ammm:Adaptive_umbrella_sampling|Multicanonical and adaptive umbrella sampling]] (Bruce) <span style="background-color: rgb(255, 102, 0);">11/4</span> == | ||
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== FEP/BAR, TI (Oscar) cancelled == | == FEP/BAR, TI (Oscar) cancelled == | ||
see | |||
* [[ammm:Free_energy_simulations|Free energy simulations (Johnny)]] | |||
* http://alchemistry.org/wiki/Main_Page | |||
Free Energy Perturbation | Free Energy Perturbation | ||
BAR | |||
Thermodynamic Integration | Thermodynamic Integration | ||
Metadynamics | |||
Metadynamics | Orthogonal Space Random Walk | ||
Orthogonal Space | |||
Read books: | Read books: | ||
*Molecular Modeling by Andrew Leach | |||
*Free energy calculations (Chipot et al ) | |||
*And papers by Ren lab. | |||
And papers by Ren lab. | |||
= Electrostatics = | = Electrostatics = | ||
== [[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> == | == [[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> == | ||
Latest revision as of 16:10, 10 May 2022
Advanced Molecular Modeling Methods
Molecular Mechanics and Force Fields (Ren, 3 lectures)
Molecular Mechanics and General force fields
Electrostatic:polarizable multipole
Ewald and vdw long range correction
AMOEBA+
Molecular Dynamics
Lagrangian and Hamiltonian (Ren)
Liouville Equation and Ergodicity
Integrator and constrain
Temperature and Pressure control
Stochastic/Langevin/Brownian/DPD dynamics
Deriving force field parameters for a new molecule/unit
Gaussian and gromacs and prodrug server (Fonner)
Amber and Antechamber (Chunli)
Metal ion and ligand parameterizations (Oscar) 9/30
QM/MM (Chistina)
Implicit Solvent approach
GB/GK (Jenny 10/12)
PB (APBS)(Yue)
Calculation of molecular surface (Maysam) 10/19
Nonpolar Solvation and hydrophobicity (Jenny 10/21)
Sampling
Free energy simulations (Johnny)
Umbrella sampling and WHAM (Yue) 10/28
REMD with gromacs (Jenny)
Multicanonical and adaptive umbrella sampling (Bruce) 11/4
Non equilibrium method and AFM simulation w gromacs (Tim) 11/11(out of town on 11/9)
Protein-ligand binding
Docking (Glide and gold) and flexibility (Maysam) 11/16
MM/PBSA with amber: theory and application(chunli) 11/18
FEP/BAR, TI (Oscar) cancelled
see
Free Energy Perturbation BAR Thermodynamic Integration Metadynamics Orthogonal Space Random Walk
Read books:
- Molecular Modeling by Andrew Leach
- Free energy calculations (Chipot et al )
- And papers by Ren lab.
Electrostatics
Comparative Analysis of RNA And Mfold (David) 11/25
Coarse-grained modeling
Gay-Berne and coarse-grain modeling (Johnny) 11/30
Rigidbody mechanics
Psudo atom RNA model (Bruce) canceled
Reaction Path and TST
Reaction path search (David) canceled
Nudged Elastic Band (NEB) in AMBER (Oscar) canceled
http://ambermd.org/tutorials/advanced/tutorial5/index.htm
http://www.quantumwise.com/documents/manuals/ATK-2008.10/chap.relax.html#chap.relax.neb.intro
Continuum method for biomolecules (Steven) canceled or merged with above
- Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods
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.
- Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis
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.
- Finite element solution of the steady-state Smoluchowksi equation for rate constant calculations
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.
- Finite element simulations of acetylcholine diffusion in neuromuscular junctions
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.
Online Resource
Gromacs tutorial
http://www.dddc.ac.cn/embo04/#Practicals