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Free energy simulation of helical transitions
Author(s) -
Ma Ning,
Chung YingHua,
van der Vaart Arjan
Publication year - 2012
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23174
Subject(s) - umbrella sampling , energy landscape , statistical physics , energy (signal processing) , molecular dynamics , force field (fiction) , sampling (signal processing) , computer science , radius , physics , computational chemistry , chemistry , quantum mechanics , thermodynamics , artificial intelligence , computer security , filter (signal processing) , computer vision
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.