1st CMM 'Users meet Developers' Workshop on QM/MM Simulations
Workshop Program

Last modified: Fri Jun 6 12:44:11 EDT 2008

Wednesday, Sep 27, 2006

Arrival of participants from out of town.

Check-in at the Latham Hotel for participants with reservations organized through the CMM.

For dinner on or close to the campus or in center city there are some suggestions for restaurants and bars.

Session 1:
8.30am: Coffee and Late Registration
8.45am: Title: Welcome and Introduction
Presenter: Axel Kohlmeyer, University of Pennsylvania
9.00am: Title: The Car-Parrinello QM/MM Implementation in CPMD
Presenter: Matteo Dal Peraro, University of Pennsylvania
9.40am: Title: GEEP: The core of the QM/MM module in CP2k
Presenter: Teodoro Laino, Universität Zürich
10.20am: Coffee Break
10.50am: Title: Exploring protein function with the Gromacs QM/MM interface
Presenter: Gerrit Groenhof, Max Planck Institute for biophysical Chemistry, Göttingen
11.30am: Title: QM/MM with Gromacs & CPMD and a new ab-initio approach to make polarizable MM atoms
Presenter: Pradip Kumar Biswas, National Institute of Health, Bethesda

Session 2:
2.00pm: Title: The Pseudobond ab initio QM/MM Method and its Applications to Histone Modifying Enzymes
Presenter: Yinkai Zhang, New York University
3.10pm: Title: (QM/MM with Dynamo)
Presenter: Shawn T. Brown, Pittsburgh Supercomputing Center
3.50pm: Coffee Break
4.20pm: Title: New QM/MM methods for RNA catalysis
Presenter: Tai-Sung Lee, University of Minnesota
5.00pm: Title: A YinYang-atom model for QM/MM calculations
Presenter: Yihan Shao, Q-Chem
5.40pm: Title: Extensions of Self-Consistent-Charge Density-Functional-Tight-Binding Model toward Accurate Descriptions of Proton Affinities, Hydrogen Bonding Interactions and Phosphate Hydrolysis Reactions
Presenter: Yang Yang, University of Wisconsin, Madison
6.20pm: Title: Discussion, Closing Remarks
Presenter: Axel Kohlmeyer, University of Pennsylvania

Session 3:
9.00: Title: Hybrid reactive CPMD based QM/MM simulations of biomolecules
Presenter: Mauro Boero, University of Tsukuba
10.00am: Coffee Break
10.30am: Title: Recent and Future Developments in QM/MM
Presenter: Ivano Tavernelli, Ecole Polytechnique Fédérale de Lausanne
11.10am: Title: CPMD: a possible treatment in the AIDS crisis
Presenter: Darrin York, University of Minnesota
11.50am: Title: Ubiquitous Coupling of Fast and Slow Modes in Biomolecules: Implications for studying polymerase catalysis using QM/MM methods
Presenter: Ravi Radhakrishnan, University of Pennsylvania

Session 4:
2.00pm: Title: Electron transfer properties of azurin from Pseudomonas Aeruginosa by hybrid QM/MM molecular dynamics simulations
Presenter: Michele Cascella, Ecole Polytechnique Fédérale de Lausanne
2.40pm: Title: Non-Adiabatic QM/MM Molecular Dynamics: Towards Photoswitchable Materials
Presenter: Marcus Böckmann, Ruhr-Universität Bochum
3.20pm: Title: TBA
Presenter: I-Feng Will Kuo, Lawrence Livermore National Laboratory
4.00pm: Coffee Break
4.30pm: Title: First-principles MD simulations of the reaction intermediates of heme catalases. Electronic consequences of heme modifications
Presenter: Mercedes Alfonso-Prieto, Parc Cientific de Barcelona
5.10pm: Title: Anharmonic Coupling in Biomolecular Crystals
Presenter: Radhakrishnan Balu, University of Maryland in Baltimore

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Session 5:
9.00am: Title: Insights into the repair mechanism of the thymine dimer in DNA from mixed QM/MM MD simulations
Presenter: Fanny Masson, Universität Zürich
9.40am: Title: QM/MM simulations of spin-coupled systems
Presenter: Eduard Schreiner, Ruhr-Universität Bochum
10.20am: Coffee Break
10.40am: Plenary Discussion.
Topics:
12.30am: Title: Closing Remarks.
Presenter: Axel Kohlmeyer, University of Pennsylvania

Departure of participants from out of town.

Check-out at the Latham Hotel for participants with reservations organized through the CMM.