Calculation of the "absolute" free energy of a beta-hairpin in an all-atom force field

  • author:

    K. V. Klenin and W. Wenzel 

  • place:

    The Journal of Chemical Physics 139, 054102 

  • date: 2013
  • We propose a new approach to calculate the conformational free energy of a macromolecule in a compact stable state in implicit solvent. The free energy is evaluated with respect to an artificial reference system without internal interactions that is confined to a small well-defined multidimensional volume of a regular shape occupying approximately the same part of the conformational space as the macromolecule of interest. We present a practical implementation of our method, successfully apply it to a β-hairpin in all-atom representation, verify the results with direct parallel tempering simulations, and discuss the possibilities of further improvements.