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Protein simulations combining an all-atom force field with a Go term

Jan H Meinke1 and Ulrich H E Hansmann1,2

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Using a variant of parallel tempering, we study the changes in sampling within a simulation, when the all-atom model is coupled to a Go-like potential. We find that the native structure is not the lowest-energy configuration in the all-atom force field. Adding a Go term deforms the energy landscape in such a way that the native configuration becomes the global minimum but does not lead to faster thermalization.


PACS

87.14.E- Proteins

87.15.A- Theory, modeling, and computer simulation

87.15.B- Structure of biomolecules

87.15.K- Molecular interactions; membrane-protein interactions

87.15.H- Dynamics of biomolecules

Subjects

Biological physics

Dates

Issue 28 (18 July 2007)

Received 14 October 2006, in final form 1 March 2007

Published 25 June 2007



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