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Use of the Metropolis algorithm to simulate the dynamics of protein chains

Author

Listed:
  • Tiana, G.
  • Sutto, L.
  • Broglia, R.A.

Abstract

The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a simplified protein model, it is possible to show that setting a threshold of 1∘ on the movement of the dihedrals of the protein backbone in a single Monte Carlo step, the mean quantities associated with the off-equilibrium dynamics (e.g., energy, RMSD, etc.) are well reproduced, while the good description of higher moments requires smaller moves. An important result is that the time duration of a Monte Carlo step depends linearly on the temperature, something which should be accounted for when doing simulations at different temperatures.

Suggested Citation

  • Tiana, G. & Sutto, L. & Broglia, R.A., 2007. "Use of the Metropolis algorithm to simulate the dynamics of protein chains," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 380(C), pages 241-249.
    • Handle: RePEc:eee:phsmap:v:380:y:2007:i:c:p:241-249
    DOI: 10.1016/j.physa.2007.02.044
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    Cited by:

    1. Wang, Gangsheng & Chen, Shulin, 2013. "Evaluation of a soil greenhouse gas emission model based on Bayesian inference and MCMC: Model uncertainty," Ecological Modelling, Elsevier, vol. 253(C), pages 97-106.

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    Keywords

    Metropolis dynamics; Protein folding;

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