Linearly scalable hybrid Monte Carlo method for conformational sampling of large biomolecules ∗

@inproceedings{Hampton2002LinearlySH,
  title={Linearly scalable hybrid Monte Carlo method for conformational sampling of large biomolecules ∗},
  author={Scott Hampton and Jes{\'u}s A. Izaguirre},
  year={2002}
}
We present a variation on the hybrid Monte Carlo (HMC) algorithm that improves the sampling of phase space. This new algorithm, called Shadow Hybrid Monte Carlo (SHMC), achieves a nearly linear scalability with system size rather than O(N5/4) of HMC. We tested both methods using vacuum and solvated biological molecules. Our results show that, for example, when sampling the conformational space of a solvated Melittin with 5123 atoms, SHMC can use time steps of 0.8 fs using leapfrog, whereas HMC… CONTINUE READING
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References

Publications referenced by this paper.
Showing 1-10 of 20 references

ProtoMol, an object-oriented framework for prototyping novel applications of molecular dynamics

  • T. Matthey, A. Ko, J. A. Izaguirre
  • Submitted to the 2003 International Conference on…
  • 2002
1 Excerpt

A direct approach to conformational dynamics based on hybrid Monte Carlo

  • C. Schutte, A. Fischer, W. Huisinga, P. Deuflhard
  • J. Comput. Phys ,
  • 1999

Leach.Molecular Modelling: Principles and Applications

  • A R.
  • 1996
1 Excerpt

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