Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

David M. Bowman
Centre for Biomedical Research, University of the Algarve
University of the Algarve, 2015


   title={Optimization of molecular dynamics simulation code and applications to biomolecular systems},

   author={Bowman, David M},



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The performance of molecular dynamics (MD) software such as GROMACS is limited by the software’s ability to perform force calculations. The largest part of this is for nonbonded interactions such as between water molecules and water molecules and solute. The determination of nonbonded interactions may account for over 90% of the total computation and real time of a simulation. The objective of this project is to greatly improve the performance of force calculations for nonbonded on a single core/processor. By doing this it is possible to raise the bar on all simulations that can be performed by GROMACS (single, multi-core or MPI). The resulting modifications need to then be verified to determine that the software still works. That it is still ‘good enough’ for performing molecular dynamics simulations.
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