2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations
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Aug 24th - 26th 2007 in Philadelphia
Workshop Program
Time line:
| Thursday, |
Aug 23, 2007. |
Arrival |
| Friday, |
Aug 24, 2007, |
"Developers Day" |
| Saturday, |
Aug 25, 2007, |
"Applications Day" |
| Sunday, |
Aug 26, 2007, |
"Users Day" / Departure |
Thursday, Aug 23, 2007
Arrival of participants.
Check-in at the Latham Hotel
for participants with reservations organized through the CMM.
For Restaurants and Bars that serve dinner on or close to the campus,
University City District, or in
Center City District.
Friday, Aug 24, 2007, "Developers Day"
- Session 1:
- Session Chair: Axel Kohlmeyer, CMM, University of Pennsylvania
- 8.30am
- Coffee and Late Registration
- 8.45am
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Title: Welcome and Introduction
Presenter: Axel Kohlmeyer
- 9.00am
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Title: Using DYNAMO to Simulate Enzymatic Reactions with Hybrid QM/MM Potential Energy Functions
Presenter: Troy Wymore, Pittsburgh Supercomputing Center
- 9.45am
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Title: ChemShell: A Modular QM/MM Simulation Package Based on the Tcl Interpreter
Presenter: Johannes Kaestner, Daresbury, UK
- 10.30am - 10.45am
- Coffee Break
- 10.45am
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Title: An overview of the QM/MM Molecular Dynamics Support in Amber 9.0
Presenter: Ross Walker, San Diego Supercomputing Center
- 11.30am
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Title: PUPIL: A New Tool for Multi-scale Simulation
Presenter: Joan Torres-Costa, Universitat
Politècnica de Catalunya, Spain
- 12.15pm
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Title: QM/MM via Common Component Architecture
Presenter: Curtis Janssen, Sandia National Labs
- 1.00pm - 3.00pm
- Lunch Break
- Session 2:
- Session Chair: Shawn Brown, Pittsburgh Supercomputing
Center
- 3.00pm
- Title: Coupling between Chemistry and Structural Transitions in Molecular Machines - Insights from QM/MM Studies
Presenter: Qiang Cui, University of Wisconsin
- 3.45pm
- Title: Substrate Selectivity in the Pore of AmtB Ammonium Transporter Studied with QM/MM Free Energy Calculations
Presenter: Guillaume Lamoureux, Concordia University, Canada
- 4.30pm - 4.45pm
- Coffee Break
- 4.45pm
- Title: Vibrational Spectroscopy within QM/MM: Dynamics of Protonated Water Networks in Bacteriorhodopsin
Presenter: Gerald Mathias, Serge Ivanov, Ruhr-Universitaet Bochum, Germany
- 5.30pm
- Title: Optimized QM/MM Capping Potentials for the Calculation of NMR Properties
Presenter: Sittipong Komin, MPIP Mainz, Germany
- 6.15pm
- Title: Closing Remarks, Announcements
- 6.30pm
- Reception
Saturday, Aug 25, 2006, "Applications Day"
- Session 3:
- Session Chair: Jochen Blumberger, University of Cambridge, UK
- 8.45am
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Title: Welcome/Announcements
Presenter: Jochen Blumberger
- 9.00am
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Title:
QM/MM with plane waves and the construction of
molecular pseudopotentials
Presenter: Mark Tuckerman, New York University
- 9.45am
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Title: QM/MM Calculations using ChemShell: Insights into Enzymatic Halogenation
Presenter: Hans-Martin Senn, University of Glasgow, UK
- 10.30am - 10.45am
- Coffee Break
- 10.45am
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Title: Applications of CPMD QM/MM to heme protein modeling
Presenter: Carme Rovira, Parc Cientific de Barcelona, Spain
- 11.30am
-
Title: QM/MM investigation of chemical reactivity of heme proteins
Presenter: Dario Estrin, University of Buenos Aires, Argentina
- 12.15pm
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Title: QM/MM Studies of metallo-beta-lactamases
Presenter: Fabio Simona, SISSA, Italy
- 1.00pm - 3.00pm
- Lunch Break
- Session 4:
- Session Chair: Teodoro Laino, University of Zürich, Switzerland
- 3.00pm
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Title: QoMMMa: A User's Perspective from Modeling Enzyme Active Sites
Presenter: Ann Schmiedekamp, Pennsylvania State University
- 3.45pm
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Title: Dissociation of Angeli's Salt in Explicit Water: An Application of the PUPIL Package as an Interface between Amber and Gaussian
Presenter: Gustavo Seabra, University of Florida
- 4.30pm - 4.45pm
- Coffee Break
- 4.45pm
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Title: Revisiting the Direct Decarboxylation Mechanism of ODCase with CP2K
Presenter: I-Feng Will Kuo, Lawrence Livermore National Laboratory
- 5.30pm
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Title: Solvent Effects on Charge Spatial Extent in DNA and Implications for Transfer
Presenter: Yves Mantz, ETHZ, Switzerland
- 6.15pm
- Title: Closing Remarks, Announcements
(Top)
Sunday, Aug 26, "Users Day"
- Session 5:
- Session Chair: Axel Kohlmeyer
- 8.45am
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Title: Welcome/Announcements
Presenter: Axel Kohlmeyer
- 9.00am
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Title: Acetylcholinesterase: 10000 ways that will not work
Presenter: Margaret Hurley, US Army Research Laboratory
- 9.30am
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QM/MM Demonstrations, Part 1
for details see the demo page.
- 10.30am - 10.45am
- Coffee Break
- 10.45am
-
QM/MM Demonstrations, Part 2
for details see the demo page.
- 12.00am - 12.30pm
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Title: Plenary Discussion, Closing Remarks.
Presenter: Axel Kohlmeyer, University of Pennsylvania
(Top)
Program of Previous Workshops
Last modified: Fri Jun 6 12:44:09 EDT 2008
