English

Metropolis simulations of Met-Enkephalin with solvent-accessible area parameterizations

Statistical Mechanics 2009-11-10 v1 Soft Condensed Matter

Abstract

We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300K K. For the energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied. The simulations are compared with one another, with simulations with a distance dependent electrostatic permittivity ϵ(r)\epsilon (r), and with vacuum simulations (ϵ=2\epsilon =2). Parallel tempering and the biased Metropolis techniques RM1_1 are employed and their performance is evaluated. The measured observables include energy and dihedral probability densities (pds), integrated autocorrelation times, and acceptance rates. Two of the ASP sets turn out to be unsuitable for these simulations. For all other systems selected configurations are minimized in search of the global energy minima, which are found for the vacuum and the ϵ(r)\epsilon(r) system, but for none of the ASP models. Other observables show a remarkable dependence on the ASPs. In particular, we find three ASP sets for which the autocorrelations at 300 K are considerably smaller than for vacuum simulations.

Keywords

Cite

@article{arxiv.cond-mat/0306435,
  title  = {Metropolis simulations of Met-Enkephalin with solvent-accessible area parameterizations},
  author = {Bernd A. Berg and Hsiao-Ping Hsu},
  journal= {arXiv preprint arXiv:cond-mat/0306435},
  year   = {2009}
}

Comments

10 pages and 8 figures