Dominik Gront and Andrzej Kolinski 2007 J. Phys.: Condens. Matter 19 036225 doi:10.1088/0953-8984/19/3/036225
Dominik Gront and Andrzej Kolinski
Show affiliationsThe parallel tempering (PT) Monte Carlo sampling scheme has already been applied to studying different systems, including spin glasses and biomolecules. In this work we examine the efficiency of PT simulations and propose an iterative procedure for the optimal selection of the replicas' temperatures. The method returns a set of temperatures for a PT simulation for which the overlap of the distribution of states (referred to as an overlap ratio) measured for every pair of adjacent replicas remains constant. The computational procedure is tested for two distinct simplified molecular models of polypeptides. The method is based on the most fundamental thermodynamic properties and therefore it could be applied to virtually any system governed by the canonical ensemble.
87.15.A- Theory, modeling, and computer simulation
36.20.Ey Conformation (statistics and dynamics)
Issue 3 (24 January 2007)
Received 4 October 2006, in final form 12 December 2006
Published 5 January 2007
Dominik Gront and Andrzej Kolinski 2007 J. Phys.: Condens. Matter 19 036225
David Langlois et al JCAP12(2008)004
Taichi Nishio et al 2008 Nanotechnology 19 035202
G Ratel and C Michotte 2003 Metrologia 40 06015
Jie Deng and Anter El-Azab 2009 Modelling Simul. Mater. Sci. Eng. 17 075010
A S Kheifets et al 2007 J. Phys.: Conf. Ser. 88 012051
Joële Viallon et al 2009 Metrologia 46 08009
Nile Oldham et al 2003 Metrologia 40 01003
G Ratel et al 2005 Metrologia 42 06005
Xiaoming Chen et al 2008 J. Micromech. Microeng. 18 037003