Performance Analyses of a Parallel Verlet Neighbor List Algorithm for GPU-Optimized MD Simulations

@article{Lipscomb2012PerformanceAO,
  title={Performance Analyses of a Parallel Verlet Neighbor List Algorithm for GPU-Optimized MD Simulations},
  author={Tyson J. Lipscomb and Anqi Zou and Samuel S. Cho},
  journal={2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom)},
  year={2012},
  pages={14-19}
}
Understanding protein and RNA biomolecular folding and assembly processes have important applications because misfolding is associated with diseases like Alzheimer's and Parkinson's. However, simulating biologically relevant biomolecules on timescales that correspond to biological functions is an extraordinary challenge due to bottlenecks that are mainly involved in force calculations. We briefly review the molecular dynamics (MD) algorithm and highlight the main bottlenecks, which involve the… CONTINUE READING

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