Starts 15 Apr 2008 12:00
Ends 15 Apr 2008 20:00
Central European Time
ICTP
Leonardo da Vinci Building Seminar Room
Strada Costiera, 11 I - 34151 Trieste (Italy)
A new molecular-dynamics algorithm for sampling the canonical distribution will be presented [1]. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. Its properties will be illustrated for Lennard-Jones and water in the solid and liquid phases. Next, a method for determining the free-energy dependence on a selected number of order parameters using an adaptive bias will be introduced [2]. This method has metadynamics and canonical sampling as limiting cases and allows for easy and rigorous error control. Finally, a new technique based on a combination of metadynamics and parallel-tempering will be discussed [3]. This scheme will be shown to be an affordable method for the computation of free-energy landscapes in biomolecules. The folding of the beta-hairpin in explicit water will then be used to illustrate the power of this technique. [1] G. Bussi, D. Donadio and M. Parrinello, J. Chem. Phys. 126, 014101 (2007) [2] A. Barducci, G. Bussi and M. Parrinello, Phys. Rev. Lett. 100, 020603 (2008). [3] G. Bussi, F. L. Gervasio, A. Laio and M. Parrinello, J. Am. Chem. Soc. 128, 13435 (2006).
  • M. Poropat