Tinkergpu:Ammm

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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

AMBER tutorial

http://ambermd.org/tutorial/

http://ambermd.org/tutorials/