MULTICANONICAL SIMULATIONS OF SOME PEPTIDES



Tarık ÇELİK

Department of Physics Engineering, Hacettepe University, Ankara, TURKEY



ABSTRACT


       In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble get trapped in states of these energy local minima. The results thus will depend strongly on the initial conditions Multicanonical method overcomes this difficulty by performing a random walk in energy space and samples much wider phase space than by conventional methods.

       A brief discussion of the multicanonical simulation method [1] will be given. The determination of the a priori unknown multicanonical weight factors by recursion will be shown. The intermediate steps of the simulation method starting from a given sequence as the input leading to the folded three dimensional structure and the minimization procedure will be shown [2]. The comparison to the canonical simulations at fixed temperature and the effectiveness of the multicanonical simulation method will be discussed and simulations of some short peptides will be presented [3].

 

REFERENCES

[1] B. A. Berg and T. Çelik, Pys. Rev. Lett. 69 (1992) 2292.
[2] F. Yaşar, T. Çelik, B. Berg and H. Meirovitch, J. Comp. Chem. 21 (2000) 1251.
[3] H. Arkın, F. Yaşar, H. Köksel, S. Çelik and T. Çelik, Int. J. Mod. Phys. C 11(8) (2000) 1595; C 12(2) (2001) 281.