Workshop/QCMM 2009
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Methods and Applications of Hybrid QC/MM Simulations to Biomolecular Systems
August 11-14, 2009
Registration is now Closed --Registration Deadline: July 7, 2009
Instructors
- Dr. Martin J. Field (Institut de Biologie Structurale)
- Dr. Troy Wymore (NRBSC, Pittsburgh Supercomputing Center)
Description
The workshop will present computational approaches for the simulation of enzymatic reactions. Lectures will be held on the relevant theoretical background including the applicability of Quantum Chemical (QC) methods for large molecules, re-parameterization of Semiempirical Molecular Orbital (SMO) methods for specific reactions, molecular mechanics (MM) force fields, hybrid QC/MM potential energy functions and simulation techniques on high performance computers. In-depth tutorials will be presented primarily with the use of the freely available pDynamo package developed in the lab of Dr. Martin J. Field and will also include developing SMO parameters for quantitatively accurate enzyme reaction simulations, the issues involved in constructing a QC/MM model and the various methods for generating energy profiles of bio-molecular reactions to determine mechanisms and structure-function relationships. Experience with pDynamo 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 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 bio-molecular systems from their own research during the workshop. Space is limited.
This workshop is supported by the NIH-National Center for Research Resources.
Topics
- Quantum Chemical Methods for Large Molecules
- Semi-empirical Molecular Orbital (SMO) Methods
- Developing Specific Reaction Parameters
- Hybrid QC/MM potential energy functions
- Umbrella sampling
- Nudged Elastic Band (NEB)
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