Journal Article

PreJuSER-6757

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Microcanonical Replica Exchange Molecular Dynamics Simulation of Proteins

Kar, P. ; Nadler, W.FZJ* ; Hansmann, U. H. E.

2009
APS College Park, Md.

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Please use a persistent id in citations: http://hdl.handle.net/2128/9321  doi:10.1103/PhysRevE.80.056703

Abstract: We present microcanonical replica exchange molecular dynamics simulations as an alternative to canonical ones. Its advantage is the easily tunable high acceptance rate for replica exchange. We present the theory, comment on its actual implementation, and demonstrate its application for a common test case, the trp-cage protein.

Keyword(s): J ; molecular biophysics (auto) ; molecular dynamics method (auto) ; proteins (auto)

Note: This work has been supported, in part, by the National Science Foundation under research Grant No. CHE-0809002. This work was started while P. K. was visiting the "Computational Biology and Biophysics" group (headed at that time by U. H.) at the John-von Neumann Institute for Computing (NIC), Julich, Germany. He would like to thank NIC for its hospitality and support, especially the use of computers at NIC, where part of the simulations were done.

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Contributing Institute(s):

1. Jülich Supercomputing Centre (JSC)

Research Program(s):

1. Scientific Computing (P41)

Appears in the scientific report 2009

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