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Parallellization of MD analysis software

David van der Spoel,Nina Fischer, Anders Gärdenäs.

With the advent of faster and faster computers the amount of data produced from molecular simulations is increasing rapidly. While the simulations themselves are often perfomed on parallel computers with thousands of processing cores, the analysis of the trajectories is typically done sequentially. Obviously there is great demand for more efficient tools, and within the GROMACS software suite a development effort is underway in order to parallellize such tools. A framework for analysis has been developed where in prinicple a master-slave approach is used and trajectory frames are handed out by a master process to slave processes for analysis. Afterwards the results are gathered and put in the right order. We aim to contribute to this by developing new tools within this framework and by porting older tools.