Dresden 2006 – scientific programme
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DY: Dynamik und Statistische Physik
DY 46: Poster
DY 46.63: Poster
Thursday, March 30, 2006, 16:00–18:00, P1
Modern Methods in Protein Simulations — •Christoph Junghans1,2 and Ulrich H.E. Hansmann2 — 1Institut für Theoretische Physik, Universität Leipzig — 2Computational Biology and Biophysics, John von Neumann Institute for Computing, Forschungszentrum Jülich
The aim of this work [1] is to study the behaviour of four advanced Monte Carlo methods in protein simulations employing a realistic ECEPP/3-based all-atom model. The implementation is based on the open source package SMMP [2]. The techniques applied were multicanonical Monte Carlo [3], parallel tempering [4], Wang-Landau sampling [5] and simulated tempering [6]. They all exhibit good properties for the high-temperature and -energy region, but still have ergodicity problems in the low-energy region due to the size of the conformation space and the rough free-energy landscape.
[1] C. Junghans, in Technical Report IB-2005-13, R. Esser (Ed.), John von Neumann Institute for Computing, J/"ulich, 2004.
[2] F. Eisenmenger, U.H.E. Hansmann, S. Hayryan and C.-K. Hu, Comp. Phys. Comm. 138 (2001) 192.
[3] B.A. Berg and T. Neuhaus, Phys. Rev. Lett. 68 (1992) 9.
[4] K. Hukushima and K. Nemoto, Jour. Phys. Soc. (Jap.) 65 (1996) 1604.
[5] F. Wang and D.P. Landau, Phys Rev. E 64 (2001) 056101.
[6] E. Marinari and G. Parisi, Europhys. Lett. 19 (1992) 451.