Phys. Rev. E 80, 056703 (2009) [8 pages]

Microcanonical replica exchange molecular dynamics simulation of proteins

Abstract

References

Citing Articles (3)

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Parimal Kar^1,*, Walter Nadler^2,†, and Ulrich H. E. Hansmann^1,‡
¹Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA
²Institute for Advanced Simulation (IAS), Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, D-52425 Jülich, Germany

Received 17 September 2009; published 18 November 2009

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.

URL:

http://link.aps.org/doi/10.1103/PhysRevE.80.056703

DOI:

10.1103/PhysRevE.80.056703

PACS:

02.70.Ns, 87.10.Tf, 87.15.Cc

^*pkar@mtu.edu

^†wnadler@fz-juelich.de

^‡hansmann@mtu.edu

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Phys. Rev. E 80, 056703 (2009) [8 pages]

Microcanonical replica exchange molecular dynamics simulation of proteins