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Summer School on ab initio Molecular Dynamics for Biomolecules

 June 9th-14th 2013 - S. Stefano di Sessanio (L'Aquila), Italy


                      Leonardo Guidoni (Università degli Studi dell'Aquila, Italy)              
      Carla Molteni (King's College London, United Kingdom)
       Daniele Varsano (Centro S3, CNR Istituto di Nanoscienze, Modena, Italy)

Local organizers
    Leonardo Guidoni (Università degli Studi dell'Aquila, Italy)
    Emanuele Coccia (Università degli Studi dell'Aquila, Italy)
          Daniele Narzi (Sapienza-Università di Roma, Italy)




Investigating how biological systems function at the atomistic level is of paramount importance not only for understanding and possibly interfering with processes that lead to diseases, but also for building nature-inspired nano-materials and nano-devices. Atomistic computer simulations are becoming increasingly useful tools to elucidate the behaviour of biological systems, complementing and expanding the experimental information which nowadays often includes structural, optical, magnetic and dynamical properties of single biomolecules.

The complexity of biological systems and processes makes them extremely challenging to investigate computationally; moreover a knowledge that goes beyond traditional disciplines is required. Simplified models for the interatomic interactions have been developed with various degrees of success. Classical force fields allow molecular dynamics (MD) simulations of large biomolecules for significant times, which have proven extremely useful in building an understanding of many processes. However, they are not accurate enough for other biological processes, where the electronic structure cannot be disregarded or considered only in an effective manner. These include photo-excitations, electron and proton transfer mechanisms, enzymatic reactions, energy transfer and other phenomena, all of which are essential ingredients for living matter, from vision to photosynthesis. Thanks to the availability of powerful computers and of efficient first principles codes, accurate and quantitative electronic structure calculations for systems of biological relevance are progressively becoming affordable. However, there is a growing need to train early stage researchers in this multi-disciplinary area, which is still not included in most academic curricula.

This Summer School focuses on the practical use of first principles electronic structure methods to investigate the structural, spectroscopic and functional properties of large biomolecules, in particular using Quantum Mechanics / Molecular Mechanics simulations based on Density Functional Theory (DFT). With the explicit inclusion of temperature effects, these methods can offer for biological systems several advantages over traditional static calculations such as helping to overcome metastable local minima by simulated annealing, including anharmonicity and configurational changes in the evaluation of molecular properties and explicitly computing the entropic effects in reaction barriers.

The School is designed mainly for graduate students and post-doctoral researchers in Physics, Chemistry and Materials Science who are familiar with ab initio molecular dynamics, but do not have much experience with biological systems. Its aim is to provide a practical guide on how to set up a molecular dynamics simulation of a biomolecule, starting from experimental structures available in the protein data bank, adding any missing parts in the structure files, selecting the portion to be treated quantum mechanically, assessing the reliability of available exchange and correlation functionals and recipes for including dispersion interactions.

An important part of the School will be devoted to the calculation of spectroscopic properties and to the common drawbacks of DFT functionals and approximations in the specific case of biological simulations, with an outlook on the potential role of more sophisticated methods (from Many Body Perturbation Theory to Quantum Monte Carlo). Moreover, the participation of experimental experts in structural biology and biomolecular spectroscopy will provide an overview of open problems in the field and on the relationships between experimental data and computational approaches. A combination of theory, computer implementation, test cases and successful state-of-the-art applications will be presented, complemented by practical simulation sessions. 

The school will be held at the Residence Il Palazzo, a building from the 17th century in S. Stefano di Sessanio (L’Aquila), one of the most beautiful villages in central Italy. The location is reachable in about 2 hours from Rome and Pescara airports.



Jochen Blumberger (University College London, United Kingdom)
Paolo Carloni (German Research School for Simulation Sciences, Jülich, Germany)
Teodoro Laino (IBM Zurich Research Laboratory, Switzerland)
Simonetta Fornarini ("Sapienza" Università di Roma, Italy)
Leonardo Guidoni (Università degli Studi dell'Aquila, Italy)
Doriano Lamba (IC-CNR, Trieste, Italy)
Carla Molteni (King's College London, United Kingdom)
Carme Rovira (ICREA, Universitat de Barcelona, Spain)
Tullio Scopigno ("Sapienza" Università di Roma, Italy)
Daniele Varsano (Centro S3, CNR Istituto di Nanoscienze, Modena, Italy)
Rodolphe Vuilleumer (UPMC, Paris, France)


From structural biology to ab initio MD

Quantum Mechanics / Molecular Mechanics

Optical properties of biological chromophores by Time Dependent Density Functional Theory

Electron transfer, Infrared and Ultrafast Raman spectroscopy in biomolecules

Computational vibrational spectroscopy

Applications of ab initio MD in biophysics, biochemistry and medicinal chemistry

Success and pitfalls of DFT in biomolecules

Correlated methods beyond DFT for ground and excited states

Preliminary Program

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Lunches (12:30 – 14:00) and dinners (19:30) will be from Sunday evening to Friday at lunch.
17:00 -18:00 Registration
20:30 – 22:00 Opening Lecture
Applications in ab initio molecular dynamics of biomolecules – Paolo Carloni
Monday - Building up the bio-system and the classical setup.
9:00 – 12:30 Lectures
- X-Ray crystallography and protein data bases I - Doriano Lamba (CNR – Trieste)
- X-Ray crystallography and protein data bases II- Doriano Lamba (CNR – Trieste)
- The classical setup - Leonardo Guidoni (Univ. de L’Aquila)
15:00 – 18:00 – Computer Tutorials
From the PDB to a reliable atomistic model. – Doriano Lamba, Leonardo Guidoni, Carla
18:30 – 19:30 Poster session with aperitif
Tuesday – Quantum Mechanics / Molecular Mechanics methods
9:00 – 12:30 Lectures
- General QM/MM methods and multigrid techniques - Teodoro Laino
- QM/MM applications – Carme Rovira
15:00 – 18:00 – Computer Tutorials
QMMM implementation in CPMD and CP2K. – Teodoro Laino, Carme Rovira
Wednesday – Spectroscopy and properties
9:00 – 12:30 Lectures
- Optical biospectroscopy – Tullio Scopigno
- Excites states in biomolecules I – Daniele Varsano
Excited states in biomolecule II - Daniele Varsano
14:30 – 16:30 Lectures
- Vibrational spectroscopy of biomolecules – Simonetta Fornarini
- Vibrational spectroscopy by AIMD – Rhodolphe Vuilleumier
17:30 – 22:00 – Social Excursion to Rocca Calascio with Social Dinner
Thursday - Spectroscopy and properties
9:30 – 13:00 Lectures
- Electron and proton transfer in biomolecules I - Jochen Blumberger
- Electron and proton transfer in biomolecules II - Jochen Blumberger
- Metadynamics I – Carla Molteni
14:30 – 15:30 Lectures
- Metadynamics II – Carla Molteni
16:00 – 18:30 Computer tutorials
- Effective normal modes - Rhodolphe Vuilleumier
Friday – Applications and Perspectives
9:00 – 11:30 Lectures
- Correlated QM/MM calculations for large biomolecules – Leonardo Guidoni
- Perspectives in ab initio MD for biomolecules. – Paolo Carloni
12:00 Shuttle bus to L’Aquila and Fiumicino/Ciampino airports (arrival in Fiumicino at 15:00)  



Lunches  (12:30 – 14:00) and dinners (19:30) will be from Sunday evening to Friday at lunch.  



17:00 ­18:00  

 - Registration  

20:30 – 22:00 Opening Lecture  

  - Applications in ab initio molecular dynamics of biomolecules - Paolo Carloni  

 Monday ­ Building up the bio‐system and the classical setup  

9:00 – 12:30 Lectures  

  ‐ X‐Ray crystallography and protein data bases I - Doriano Lamba (CNR – Trieste)  

  ‐ X‐Ray crystallography and protein data bases II - Doriano Lamba (CNR – Trieste)  

  ‐ The classical setup ‐ Leonardo Guidoni (Univ. de L’Aquila)  

15:00 – 18:00 – Computer Tutorials  

  - From  the  PDB  to  a  reliable  atomistic  model - Doriano  Lamba,  Leonardo  Guidoni,  Carla Molteni  

18:30 – 19:30 Poster session with aperitif  

 Tuesday – Quantum Mechanics / Molecular Mechanics methods  

9:00 – 12:30 Lectures  

  ‐ General QM/MM methods and multigrid techniques ‐ Teodoro Laino   

  ‐ QM/MM applications – Carme Rovira  

15:00 – 18:00 – Computer Tutorials  

  - QM/MM implementation in CPMD and CP2K - Teodoro Laino and Carme Rovira  


 Wednesday – Spectroscopy and properties  

9:00 – 12:30 Lectures  

  ‐ Optical biospectroscopy - Tullio Scopigno   

  ‐ Excites states in biomolecules  I - Daniele Varsano  

  ‐ Excited states in biomolecules II ‐ Daniele Varsano 

14:30 – 16:30 Lectures  

  ‐ Vibrational spectroscopy of biomolecules - Simonetta Fornarini  

  ‐ Vibrational spectroscopy by AIMD - Rhodolphe Vuilleumier  

17:30 – 22:00 – Social Excursion to Rocca Calascio with Social Dinner  


 Thursday – Spectroscopy and properties  

9:30 – 13:00 Lectures  

 ‐ Electron and proton transfer in biomolecules I ‐ Jochen Blumberger  

 ‐ Electron and proton transfer in biomolecules II ‐ Jochen Blumberger  

 ‐ Metadynamics I – Carla Molteni  

14:30 – 15:30 Lectures  

  ‐ Metadynamics II - Carla Molteni  

16:00 – 18:30 Computer tutorials  

  ‐ Effective normal modes ‐ Rhodolphe Vuilleumier  


 Friday – Applications and Perspectives  

9:00 – 11:30 Lectures  

  ‐ Correlated QM/MM calculations for large biomolecules - Leonardo Guidoni  

  ‐ Perspectives in ab initio MD for biomolecules - Paolo Carloni  


12:00  Departure  

Shuttle bus to L’Aquila and Fiumicino/Ciampino airports (arrival in Fiumicino at 15:00) 





Application form

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The deadline for registration and poster abstract submission is 12th May 2013.The number of participants is limited to about 30 students. Accepted participants will be notified by 15th May 2013. A limited number of fellowships are available to fully cover the accommodation and food costs for the students. The deadline for fellowship applications is 29th April 2013.
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Acommodation in S. Stefano di Sessanio

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S. Stefano di Sessanio has been named one of the most beatiful villages in Italy ("Borghi più belli d'Italia"). You can find here a small description of the village and its historical and cultural background. The accomodation will be the Residence Il Palazzo  (choose your language on the bottom of the home page) and La casa di su.

 The cost per day for meals (breakfast, coffee breaks, lunch and dinner) and accomodation is 65 € per person in a double room (325 € for all the period) and 80 € per person in a single room (400 € for all the period). A certain number of fellowships fully covering meals and accommodation for the 5 days will be awarded to selected participants who request finantial support. The deadline for the fellowship application has been extended to 29th April 2013.



How to arrive at S. Stefano di Sessanio

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By Car (From Rome)

Follow the A24 Highway from Rome to “L'Aquila Ovest” Exit. At the first roundabout turn right towards the Center of L'Aquila, and afterwards turn left still in the same direction; through the state road SS17. Keeping on the SS17 road you will pass through the towns of Bazzano, San Gregorio, Poggio Picenze, until the crossroad between Barisciano and Castelnuovo. Follow the direction to Barisciano directly to S. Stefano di Sessanio. The Residence Il Palazzo is along the main road, at the end of the village.

By Car (From L'Aquila)

Take the state road SS17 in the direction towards Bazzano: you will pass the towns of San Gregorio, Poggio Picenze, until the crossroad between Barisciano and Castelnuovo. Follow the direction to Barisciano directly to S. Stefano di Sessanio. The Residence Il Palazzo is along the main road, at the end of the village.

By Bus (From Rome Airports)

From Fiumicino: A direct bus to L'Aquila can be found at the Arrivals T3 terminal, at the tourist bus parking. In L'Aquila there will be only one stop in front of the Amiternum Hotel just after the L'Aquila Ovest exit of the highway. Detailed information can be found here. The ticket costs 16 €, leaving at 11.00 , 14.00 , 16.00 , 19.00 , 21.30 from Fiumicino.

From Ciampino: At the Entrance of the Airport, towards the roundabout, there is a Cotral bus stop were you can take the direct bus to the Amiternum Hotel just after the L'Aquila Ovest exit (first stop after the highway). Detailed information can be found here. The ticket costs 16 €, leaving at 11.30 , 14.30 , 16.30 , 19.30 , 22.00 from Ciampino.

By Bus (From Rome Train Stations)

From Termini Station: Take the metro B from Termini to Tiburtina train station and follow the instructions below.

From Tiburtina Station: About 200 meters in front of the station, crossing the road, there is the bus station, were you can find a direct bus for L'Aquila (Amiternum Hotel). The bus will leave at 11.00, 12.25, 13.30, 15.00, 18.00, 19.00, 19.30, 20.30, 21.30, 22.00, 23.00 on Sunday. The complete timetable can be found here. Get off at the first stop in L'Aquila (in front of the Amiternum hotel).

(On Sunday 9th and Friday 14th in correspondence with the arrival of arport busses, shuttle busses will be organised from/to the Amiternum Hotel to/from S. Stefano di Sessanio.)


Webmaster Emanuele Coccia

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