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< | '''Advanced Molecular Modeling Methods''' | ||
= ''Molecular Mechanics and Force Fields (Ren, 3 lectures)'' = | |||
== [[ammm:Mm_gff|Molecular Mechanics and General force fields]] == | |||
== [[ammm:Mm_mpole|Electrostatic:polarizable multipole]] == | |||
== [[ammm:Mm_ewald|Ewald and vdw long range correction]] == | |||
== [[ammm:Mm_aplus|AMOEBA+]] == | |||
= ''MD (Ren, 4 lectures)'' = | |||
== [[ammm:Md_ham|Lagrangian and Hamiltonian]] (Ren) == | |||
== [[ammm:Md_erg|Liouville Equation and Ergodicity]] == | |||
== [[ammm:Md_integrator|Integrator and constrain]] == | |||
== [[ammm:Md_tp|Temperature and Pressure control]] == | |||
== Stochastic/Langevin/Brownian/DPD dyanmics == | |||
GLE.pdf | |||
= ''Deriving force field parameters for a new molecule/unit'' = | |||
== [[ammm:Ff_gau_grom_prdrug|Gaussian and gromacs and prodrug server (Fonner)]] == | |||
== [[ammm:Ff_amber_ligand_parameter|Amber and Antechamber (Chunli)]]== | |||
== [[ammm:Lig_ion_params|Metal ion and ligand parameterizations (Oscar) 9/30]] == | |||
= [[ammm:QM/MM|QM/MM (Chistina)]] = | |||
= ''Implicit Solvent approach'' = | |||
== [[ammm:Gb_gk|GB/GK (Jenny 10/12)]] == | |||
== [[ammm:PB_(APBS)|PB (APBS)(Yue)]] == | |||
== [[ammm:Molecular_surfaces|Calculation of molecular surface (Maysam)]] <span style="background-color: rgb(255, 102, 0);">10/19</span> == | |||
== [[ammm:Nonpolar_solvation|Nonpolar Solvation and hydrophobicity (Jenny 10/21)]] == | |||
= ''Sampling'' = | |||
== [[ammm:Free_energy_simulations|Free energy simulations]] (Johnny) <span style="background-color: rgb(255, 102, 0);">10/26</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 (Fonner)]] == | |||
== [[ammm:REMD_jenny|REMD with gromacs (Jenny)]] == | |||
== Headline text == | |||
== [[ammm:Adaptive_umbrella_sampling|Multicanonical and adaptive umbrella sampling]] (Bruce) <span style="background-color: rgb(255, 102, 0);">11/4</span> == | |||
== [[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> == | |||
= ''Protein-ligand binding'' = | |||
== [[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> == | |||
== [[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> == | |||
== FEP/BAR, TI (Oscar) cancelled == | |||
Free Energy Perturbation | |||
Thermodynamic Integration | |||
Metadynamics | |||
Orthogonal Space Randowm Walk | |||
Read books: | |||
1. Molecular Modeling by Andrew Leach | |||
2. Free energy calculations (Chipot et al ) | |||
And papers by Ren lab. | |||
= Electrostatics = | |||
== [[ammm:VSE|<span style="color: rgb(0, 0, 0);">New procedure to study electrostatic fields in proteins (Chistina)</span>]]<span style="background-color: rgb(255, 102, 0);">'''11/23'''</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> == | |||
= ''Coarse-grained modeling'' = | |||
== [[ammm:Coarse_grain_modeling|Gay-Berne and coarse-grain modeling (Johnny) 11/30]] == | |||
== [[ammm:Rigid_body_MD_(Steven_12/2) | 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://ambermd.org/tutorials/advanced/tutorial5/index.htm] | |||
[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] | |||
= 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 http://www.dddc.ac.cn/embo04/#Practicals] | |||
== AMBER tutorial == | |||
[http://ambermd.org/tutorial/ http://ambermd.org/tutorial/] | |||
[http://ambermd.org/tutorials/ http://ambermd.org/tutorials/] | |||
Latest revision as of 23:03, 9 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+
MD (Ren, 4 lectures)
Lagrangian and Hamiltonian (Ren)
Liouville Equation and Ergodicity
Integrator and constrain
Temperature and Pressure control
Stochastic/Langevin/Brownian/DPD dyanmics
GLE.pdf
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) 10/26
Umbrella sampling and WHAM (Yue) 10/28
REMD with gromacs (Fonner)
REMD with gromacs (Jenny)
Headline text
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
Free Energy Perturbation
Thermodynamic Integration
Metadynamics
Orthogonal Space Randowm Walk
Read books:
1. Molecular Modeling by Andrew Leach
2. Free energy calculations (Chipot et al )
And papers by Ren lab.
Electrostatics
New procedure to study electrostatic fields in proteins (Chistina)11/23
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