title: 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.
authors.affiliation: Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Ma
authors.forename: Ying-Hua
authors.initials: YH
authors.lastname: Chung
authors.forename: Arjan
authors.initials: A
authors.lastname: van der Vaart
mesh_terms: D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins; D004247:DNA