Scalability of Molecular Dynamics Simulations of Lipopolysaccharide Membranes Using the GROMACS Software Package on Different Architectures

• Frederico Pontes UFPB
• Victor Rusu UFPB
• Roberta Dias UFPB
• Gabriel Hora UFPB
• Denys Santos UFPB
• Laércio Pol-Fachin UFPB
• Roberto Lins UFPB
• Thereza Soares UFPB

Resumo

We present benchmarks and efficiency estimates for the GROMACS package performing molecular dynamics (MD) simulations of lipopolysaccharide membranes on different computer platforms (Intel Xeon, BlueGene/P, AMD Opteron Interlagos and Barcelona). Satisfactory parallel scaling was achieved in all architectures, even when it was compiled without vector instruction support on BG/P. GROMACS v 4.x scaled well up to 2048 cores for a system containing over one million atoms. Atom/core performance at different platforms was also assessed. It shows that MD simulation of large complex biological systems can greatly benefit from petascale computing and, if adequately ported, can take appreciable advantage of hybrid hardware.

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