Initial conceptual design indicates that simulation will be performed on controlled machines, due to additional software complexity. Simulation analysis will be distributed to end-user workstation machines, in the form of a BOINC client. The current implementation uses GROMACS (version 3.3) to perform the molecular dynamics simulation, writing and reading the GROMACS specific binary formats. Our code is called before and after the GROMACS executable, to set up initial conditions and to update the simulation state (such as molecular bonding) before resubmitting to the GROMACS binary for the next stage of processing.
We are currently focusing effort on, and looking for assistance with:
Server side simulation condition generation
Simulation result distribution
Distributed BOINC client
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