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Free energy simulation of helical transitions

Authors

  • Ning Ma,

    1. Department of Chemistry, University of South Florida, 4202 E Fowler Avenue, CHE 205, Tampa, Florida 33620
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    • These authors contributed equally to this work.

  • Ying-Hua Chung,

    1. Department of Chemistry, University of South Florida, 4202 E Fowler Avenue, CHE 205, Tampa, Florida 33620
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    • These authors contributed equally to this work.

  • Arjan van der Vaart

    Corresponding author
    1. Department of Chemistry, University of South Florida, 4202 E Fowler Avenue, CHE 205, Tampa, Florida 33620
    • Department of Chemistry, University of South Florida, 4202 E Fowler Avenue, CHE 205, Tampa, Florida 33620
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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.

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