Free energy simulation of helical transitions

Abstract

An umbrella sampling method for the calculation of free energies for helical transitions is presented. The method biases structures toward helices of a desired radius and pitch. Although computationally complex, the method has negligible overhead in actual applications. To illustrate the method, calculations of the helical free energy landscape of several peptides are presented for both the CHARMM and the AMBER force fields. © 2012 Wiley Periodicals, Inc. A new umbrella sampling method was developed to calculate free energies of helical transitions. With this method, the free energy landscape as a function of the helical radius and pitch was calculated for four peptides using the AMBER and CHARMM force fields. Copyright © 2012 Wiley Periodicals, Inc.