Organisers

• Fabio Pietrucci (CECAM-EPFL Lausanne, Switzerland)
• Giovanni Bussi (SISSA, Italy)
• Davide Branduardi (Italian Institute of Technology, Italy)

Supports

   CECAM

Description

Application deadline is May 31, 2010. For further information and to see a preliminary program, see sites.google.com/site/plumedtutorial2010

Computer simulations at the atomic scale play a fundamental and ever-increasing role in molecular biology, chemistry, and condensed-matter physics. However, accurate simulation techniques typically have a large computational cost, which strongly reduces their scope in the study of rare events like, e.g., protein folding, drug binding, chemical reactions, and phase transitions. To enlarge the timescales which can be investigated by atomistic simulations, several powerful enhanced-sampling and free-energy calculation methods have been developed in recent years. Different approaches have been implemented on a variety of existing computer simulation codes, and it often occurs that a given technique is re-implemented multiple times in the same program by different researchers.

PLUMED (see http://merlino.mi.infn.it/~plumed) is a freely-available series of routines which can be automatically interfaced with the most common molecular dynamics programs (Gromacs, Namd, Dl_poly, Amber, etc.) and which enables to perform free-energy calculations by using state-of-the-art enhanced sampling techniques, i.e. metadynamics (in all its variants), umbrella sampling, and Jarzynski method. This facilitates the comparison among different enhanced sampling techniques and permits to choose freely the simulation program most appropriate for each specific application and computer resources available. PLUMED is developed and maintained by a team of computational scientists including the developers of some of the latter techniques, and it benefits by the daily feedback from a rapidly growing community of users (>320 independent downloads as of Jan 2010).

Scientific Objectives

• Present prominent free-energy calculation methods to young researchers, with examples of applications.
• Train the participants to interface PLUMED with popular molecular dynamics codes.
• Train the participants to perform realistic free-energy calculations tailored on their specific scientific problems.
• Train the participants to critically assess the accuracy and reliability of their results (error estimation, comparison of different approaches).
• Train the participants to modify PLUMED in order to introduce collective variables tailored on their specific atomic systems.
• Promote the reproducibility of scientific results, namely free-energy calculations, using standardized algorithms and systematically comparing different enhanced sampling techniques and molecular dynamics programs.
• Promote the communication and cross-fertilization among different computational groups in Europe and in the rest of the world.

References

Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603 (2008).
Bonomi, Barducci, Parrinello, J. Comp. Chem. 30, 1615 (2009).
Bonomi, Branduardi, Bussi, Camilloni, Provasi, Raiteri, Donadio, Marinelli, Pietrucci, Broglia and Parrinello, Comp. Phys. Comm. 180, 1961 (2009).
Branduardi, Gervasio and Parrinello, J. Chem. Phys. 126, 054103 (2007).
Bussi, Gervasio, Laio, and Parrinello, J. Am. Chem. Soc. 128, 13435 (2006).
Bussi, Laio and Parrinello, Phys. Rev. Lett. 96, 090601 (2006).
Laio and Gervasio, Rep. Prog. Phys. 71, 126601 (2008).
Laio and Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
Laio, Rodriguez-Fortea, Gervasio, Ceccarelli, and Parrinello, J. Phys. Chem. B 109. 6676 (2004).
Piana and Laio, J. Phys. Chem. B 111, 4553 (2007).
Marinelli, Pietrucci, Laio, and Piana, PLoS Comput. Biol. 5(8), e1000452 (2009).
Parrinello, Eppur si muove, in Physical Biology: From Atoms to Medicine, p 247 (2008).
Pietrucci and Laio, J. Chem. Theory Comput. 5, 2197 (2009).
Raiteri, Laio, Gervasio, Micheletti, and Parrinello, J. Phys. Chem. B 110, 3533 (2006).
Torrie and Valleau, J. Comput. Phys. 23, 187 (1977).