Tese de doutoramento, Bioquimica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015The 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.Virtual Strategy, Inc., Boston, M
