Microcanonical replica exchange molecular dynamics simulation of proteins

Parimal Kar, Walter Nadler, and Ulrich H. E. Hansmann
Phys. Rev. E 80, 056703 – Published 18 November 2009

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.

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  • Received 17 September 2009

DOI:https://doi.org/10.1103/PhysRevE.80.056703

©2009 American Physical Society

Authors & Affiliations

Parimal Kar1,*, Walter Nadler2,†, and Ulrich H. E. Hansmann1,‡

  • 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

  • *pkar@mtu.edu
  • wnadler@fz-juelich.de
  • hansmann@mtu.edu

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Issue

Vol. 80, Iss. 5 — November 2009

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