NRBSC.org

Methods and Applications of Hybrid QM/MM Simulations to Biomolecular Systems

September 10 - 13, 2007

HONORARY LECTURER:

INSTRUCTORS:

  • Dr. Troy Wymore (NRBSC)
  • Dr. Shawn Brown (PSC)


APPLICATION DEADLINE: August 3, 2007
Click here to apply

workshop image

DESCRIPTION:
The workshop will explore computational approaches for the simulation of enzymatic reactions. The course will present the relevant theoretical background including ab initio and semiempirical molecular orbital methods, density functional theory, molecular mechanics force fields, hybrid Quantum Mechanical/Molecular Mechanical potential energy functions, and simulation techniques on high performance computers. Case studies based on determining the free energy profile for a reaction in the gas phase, in water (using both implicit and explicit solvent) and in an enzyme active site will be presented using primarily the DYNAMO library. Experience with DYNAMO is helpful but not a prerequisite for attendance.

The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have some experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on biomolecular systems from their own research during the workshop.

TOPICS
Model Chemistries
Transition state searches
Implicit solvent models
Parameterization of Semiempirical Methods
Hybrid QM/MM potentials
Umbrella sampling
Nudged Elastic Band
FINANCIAL INFORMATION TENTATIVE AGENDA READING LIST


Workshop Wiki (PSC network only)

TUTORIALS

Tutorial 1: Quantum Chemical Tutorial

Tutorial 2: Proton Transfer between methylthiolate and phenol in a box of water

Tutorial 3: Construction of a solvated enzyme



PRESENTATIONS

Intro to Abinitio (Brown)

Density Functional Theory (Brown)

Hybrid Potentials Basics (Field)

Hybrid Potentials Reactions (Field)

Hybrid Potentials Reactions II (Field)

Hyrbid Potentials Reactions III (Field)

Using Dynamo to Simulate Enzyme Reactions (Wymore)