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Barcelona Workshop 2012

A pDynamo workshop is to be held in Barcelona from the 12th to the 14th September 2012 at CESCA. It will consist of a number of presentations by invited speakers and members of the pDynamo community, together with a number of practical sessions using pDynamo. Students and those new to pDynamo are especially welcome. Partial support for the workshop is being provided by the XRQTC.
XRQTC

Please contact one of the organizers if you wish to attend or you require further information - either Ramon Crehuet, Martin Field or Troy Wymore.

Speakers

A provisional list of speakers with titles is:

 Aleksandrov, Alexey  Ecole Polytechnique, Paris  Reaction path methods
 Arantes, Guilherme  University of Sao Paulo  QC/MM simulations of metalloproteins
 Crehuet, Ramon
 IQAC, Barcelona
 QC/MM simulations with ab initio approaches
 Field, Martin
 IBS, Grenoble
 Introduction to pDynamo
 Keinan, Shahar  Tera Disc, North Carolina  pDYNAMO workflow: QM/MM on multiple targets, multiple ligands on the Azure cluster
 Marti, Sergio
 University of Castellon
 Applications and insights on enzymatic processes derived from studies with Dynamo. A practical guide. Part I
 Moliner, Vicent  University of Castellon  Applications and insights on enzymatic processes derived from studies with Dynamo. A practical guide. Part II
 Raos, Guido  Milan Polytechnique  Modeling of crystal structures
 Rovira, Carme
 University of Barcelona
 Using CPMD QM/MM metadynamics to study enzyme mechanisms
 Wymore, Troy
 PSC, Pittsburgh
 Using pDynamo to investigate enzyme dynamics and reactions

Program

Day 1: Using pDynamo for Simulation of Molecular Systems

09:00-09:30 Ramon Crehuet: Opening remarks
09:30-10:30 Martin Field: Introduction to pDynamo
10:30-10:45 Coffee Break
10:45-12:30 Martin Field: Hybrid potentials
12:30-13:30 Lunch Break
13:30-14:30 Troy Wymore: Using pDynamo to investigate enzyme dynamics and reactions
14:30-14:45 Coffee Break
14:45-17:00 Guilherme Arantes: QC/MM simulations of metalloproteins

Day 2: Modeling Reactions with Hybrid Potentials I

09:00-10:00 Guido Raos: Modeling of crystal structures
10:00-10:30 Coffee Break
10:30-12:00 Shahar Keinan: pDYNAMO workflow: QM/MM on multiple targets, multiple ligands on the Azure cluster
12:00-12:30 Troy Wymore: The GTK pDynamo GUI
12:30-13:30 Lunch Break
13:30-14:30 Sergio Marti: Applications and insights on enzymatic processes derived from studies with Dynamo. A practical guide. Part I
14:30-14:45 Coffee Break
14:45-15:45 Vicent Moliner: Applications and insights on enzymatic processes derived from studies with Dynamo. A practical guide. Part II
15:45-17:00: Round Table Discussion: Future directions and developments.

Day 3: Modeling Reactions with Hybrid Potentials II


09:00-10:00 Alexey Aleksandrov: Reaction path methods
10:00-10:30 Coffee Break
10:30-12:30 Ramon Crehuet: QC/MM simulations with ab initio approaches
12:30-13:30 Lunch Break
13:30-14:30 Carme Rovira: Using CPMD QM/MM metadynamics to study enzyme mechanisms
14:30-15:00 Coffee Break
15:00-16:30 Discussion and Conclusions

Accommodation

No accommodation has been arranged specifically for the workshop but some suggestions for hotels and residences are given below. Note that the CESCA is located about 20 minutes or so from the center of Barcelona by metro.

Bonanova Park
 A hotel relatively close to CESCA
Catalonia Rigoletto (****)
 "
Husa Arenas (****)  "
NH Rallye (***)
 "
Torre-Girona  A luxury university residence close to CESCA
Col.legis Majors  A university student residence
El Jardi
 A hostel near the center
Pere Tarrés A hostel approximately 20 minutes from CESCA by public transport