The study of helix–coil transition of polyalanine with single histogram method

We have studied helix–coil transition in all-atom model of polyalanine in vacuum and distance-dependent dielectric function solvent model. Molecules of up to length 30 residues were investigated by Monte Carlo method. The single histogram method was performed to obtain thermodynamic quantities such...

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Bibliographic Details
Published inComputer physics communications Vol. 175; no. 9; pp. 604 - 611
Main Authors Yaşar, F., Demir, K.
Format Journal Article
LanguageEnglish
Published Elsevier B.V 01.11.2006
Subjects
Helix–coil transition
Molecular simulation
Polyalanine
Single histogram method
Solvent model
75.40.Gb
Molecular simulation
Polyalanine
Solvent model
87.15.-v
Helix–coil transition
Single histogram method
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Summary:We have studied helix–coil transition in all-atom model of polyalanine in vacuum and distance-dependent dielectric function solvent model. Molecules of up to length 30 residues were investigated by Monte Carlo method. The single histogram method was performed to obtain thermodynamic quantities such as average energy and specific heat. We have also calculated probability distribution of energy and Binder cumulant as well as autocorrelation times for both case in order to identify the order of phase transition by using finite-size scaling arguments. Even though the probability distributions showed a single Gaussian peak, especially for this solvent model, the significant differences between the vacuum and solvent model were observed at their specific heat maximum values and Binder cumulant behaviors. While Binder cumulant has a deep valley for vacuum, it is not sensitive for the distance-dependent dielectric function solvent model. Our data are consistent with recently obtained results for polyalanine by multicanonical method.
ISSN:0010-4655
1879-2944
DOI:10.1016/j.cpc.2006.07.008