Move set, algorithm, and folding kinetics of Monte Carlo simulations for lattice polymers.pdf

a r X i v : c o n d - m a t / 0 5 1 2 2 6 3 v 1 [ c o n d - m a t .s o f t ] 1 3 D e c 2 0 0 5 Move set, algorithm, and folding kinetics of Monte Carlo simulations for lattice polymers Yu-Pin Luo, Ming-Chang Huang? and Yen-Liang Chou Department of Physics, Chung-Yuan Christian University, 32023 Chungli, Taiwan Tsong-Ming Liaw Computing Centre, Academia Sinica, 11529 Taipei, Taiwan (Dated: February 2, 2008) The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is given. The new method is shown to satisfy the detailed balance and converge efficiently towards thermal equilibrium. A new quantity, employed from the continuous time Monte Carlo method, is introduced to identify effectively the kinetic traps of foldings. PACS numbers: The problem how proteins fold, in milliseconds to sec- onds, into unique and stable structures with definite bio- logical functions has recently become intriguing to the biophysicians[1]. The kinetic feature of such problem amounts to the characteristics of the folding paths. Sub- ject to this, considerable progress have been achieved through numerical studies of lattice heteropolymers in two or three dimensions[2, 3, 4]. Although oversimpli- fied, characteristic features obtained from the simula- tions, such as folding funnel[5, 6], folding bottleneck[2] and kinetic traps[3, 7], have provided much insights to the kinetic process. However, there exists some suspicions about the simulation method[8, 9, 10] and few ambigui- ties in the move sets adopted for the simulations[3, 10]. For the former, question about implementing the kinetic Monte Carlo algorithm was raised and some implemen- tations were shown to violate the condition of detailed balance[9]. For the latter, Chan and Dill[3] and Hoang and Cieplak[10] stressed the strong dependence of the folding lands