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

doi:10.1088/0953-8984/19/28/285215

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

Jan H Meinke et al 2007 J. Phys.: Condens. Matter 19 285215 (9pp) doi: 10.1088/0953-8984/19/28/285215

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Jan H Meinke¹ and Ulrich H E Hansmann^1,2
¹ John-von-Neumann Institute for Computing, Forschungszentrum Jülich, D-52425 Jülich, Germany
² Department of Physics, Michigan Technological University, Houghton, MI 49931, USA
E-mail: j.meinke@fz-juelich.de and u.hansmann@fz-juelich.de

Abstract. 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.

Print publication: Issue 28 (18 July 2007)
Received 14 October 2006, in final form 1 March 2007
Published 25 June 2007

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

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