PRACE
Published December 2, 2012 | Version v1
Working paper Open

Analysis of symplectic integration algorithms with variable step size for petascale biomolecular simulations

Creators

  • 1. National Centre for Supercomputing Applications, Acad. G. Bonchev Str, Bl. 25-A, 1113 Sofia, Bulgaria

Contributors

Description

Based on the analysis of the performance, scalability, work-load increase and distribution of the MD simulation packages GROMACS and NAMD for very large systems and core numbers, we evaluate the possibilities for overcoming the deterioration of the scalability and
performance of the existing MD packages by implementation of symplectic integration algorithms with multiple step sizes.

Files

Analysis of symplectic integration algorithms with variable step size for petascale biomolecular simulations.pdf

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Additional details

Funding

PRACE-1IP – PRACE - First Implementation Phase Project 261557
European Commission