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J Chem Phys. 2013 Aug 7;139(5):054102. doi: 10.1063/1.4817195.

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

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Steinbuch Centre for Computing, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany.


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.


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