Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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Our poster about GROMACS in the cloud presented by Mikael Trellet has won the poster prize at the International Symposium on Cloud and Grid computing 2017 in Taipei.

Under the WeNMR project we have previously published our grid-enabled GROMACS web portal[1]. GROMACS [2] is one of the world most used molecular dynamics suite. We demonstrated in this poster a new version of our GROMACS web portal that is now directly connected to the EGI FedCloud infrastructure via DIRAC [3], an interware that allows institutions to use grid or cloud resources through a simplified and generic framework. The service integrates the necessary EGI services and infrastructure for the Virtual Organization, including BioExcel, West-Life and others.

[1] Marc van Dijk, Tserk A. Wassenaar and Alexandre M.J.J. Bonvin. A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations. J. Chem. Theo. Comput., 8, 3463-3472 (2012).

[2] Abraham, Mark James, et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1 (2015): 19-25.

[3] Méndez Muñoz, Víctor et al. How to Run Scientific Applications with DIRAC in Federated Hybrid Clouds. ADVCOMP 2013: The Seventh International Conference on Advanced Engineering Computing and Applications in Sciences. 73-78 Blomer, Jakob, et al. Distributing LHC application software and conditions databases using the CernVM file system. Journal of Physics: Conference Series. Vol. 331. No. 4. IOP Publishing, 2011.