9-12 May 2017
Europe/Rome timezone

Molecular dynamics of proteins in the cloud

Not scheduled


Dr Andrea Giachetti (CIRMMP) Dr Antonio Rosato (CIRMMP)


A key computational technique in Structural Biology is Molecular Dynamics (MD), a computer simulation of the motion of atoms and molecules as a function of time. MD simulations capture the behavior of biological macromolecules in full atomic detail using statistical thermodynamics laws. Such simulations serve as a computational microscope, revealing biomolecular mechanisms at various spatial and temporal scales. In our work, we have implemented and tested a variety of approaches to the use of grid and cloud computational infrastructures for MD simulations. Previously, we implemented a web interface to setup MD simulations that were then executed on the European Grid Infrastructure [1]. We then exploited the technologies developed by the INDIGO-Datacloud project to expand both the types of computational infrastructures that can be used and the portfolio of services. For this we implemented the AmberTools suite [2] as a container for Docker. Next, we implemented the use of cloud storage resources to save trajectories and perform their analysis and comparison with experimental data, such as NMR order parameters. Cloud storage uses the Onedata solution, which can work with large files such as those typically output by MD simulations. The simulations and analyses are set up and the results provided via web interfaces, so that the user does not need to know which kind of infrastructure is used. The web interface is accessed by the users using the IAM solution provided by INDIGO-Datacloud. Cloud computing is exploited for specific applications. In this case, we used an OpenStack private cloud and OpenStack4j was adopted for provisioning and control of the instances. In the future we will migrate this to the FutureGateway system. [1] A Grid-enabled web portal for NMR structure refinement with AMBER. Bertini I, Case DA, Ferella L, Giachetti A, Rosato A. [2] http://ambermd.org/

Primary authors

Dr Andrea Giachetti (CIRMMP) Dr Antonio Rosato (CIRMMP)


Mr Davide Sala (University of Florence)

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