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

TL;DR

This study evaluates various solvent-accessible area parameterizations in Metropolis simulations of Met-Enkephalin, comparing their performance and effects on energy minima and autocorrelation times.

Contribution

It systematically compares nine ASP sets and electrostatic models in peptide simulations, highlighting their impact on simulation efficiency and results.

Findings

Two ASP sets are unsuitable for simulations.

Global energy minima are found in vacuum and ε(r) models, not ASP models.

Some ASP sets reduce autocorrelation times significantly.

Abstract

We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300$ 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 $\epsilon (r)$, and with vacuum simulations ($\epsilon =2$). Parallel tempering and the biased Metropolis techniques RM$_1$ 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 $\epsilon(r)$ 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.