Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA.
J Comput Chem. 2013 Mar 30;34(8):640-5. doi: 10.1002/jcc.23174. Epub 2012 Nov 5.
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.
提出了一种用于计算螺旋转变自由能的伞形采样方法。该方法使结构偏向于所需半径和螺距的螺旋。尽管计算复杂，但该方法在实际应用中几乎没有开销。为了说明该方法，针对 CHARMM 和 AMBER 力场，给出了几个肽的螺旋自由能势面的计算结果。
