[Dock-fans] Dock is too slow even in parallel using MPI

Phan, Jason jason.phan at Vanderbilt.Edu
Mon Apr 16 17:43:36 PDT 2012

Dear All,

What are the parameters that can be manipulated to improve the virtual docking performance without compromising the quality of the dock results? My grid box is pretty small, covering ~11 spheres and pretty much default values were used for all the parameters. Using parallel processing with dock5mpi over 4 nodes, 8 processors each, the speed is terribly slow, e.g. 1-3 min per ligand. I tried lowering the  max_orientations, simplex iterations, 1 conformer written, no clustering etc... and it improved some. I'm wondering if there are better ways to speed things up a lot more.


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