| Regional Biophysics Meeting 2005, March 16-20, Zreče, Slovenia | [ComputModel] |
A parallel implementation of the Split Integration Symplectic Method (SISM) molecular dynamics (MD) integration algorithm, which allows using longer simulation timesteps due to its analytical treatment of high-frequency molecular motions, for multiple MD-GRAPE II MD processors is described. MD-GRAPE II processors are dedicated to calculating non-bonded interactions among all the atoms in a system. The implemented MD computer program uses the MD-GRAPE II processor to calculate intermolecular Coulomb and van der Waals forces and uses the host computer processor for other calculations, including analytically calculating intramolecular forces. The parallel implementation uses multiple MD-GRAPE II processors in different computers and uses a gigabit Ethernet network for communicating among them. We used molecular systems with approximately a million water molecules to demonstrate the performance of our implemention. The effectiveness of combining the SISM with the MD-GRAPE II processor is established by comparing the speed of the described computer program with the speeds of computer programs not implementing the SISM or using the MD-GRAPE II processors. Results show that the SISM, combined with the MD-GRAPE II processor, allows much faster MD simulations than standard methods and standard computers. The speedup due to parallelization is shown to be significant when using multiple MD-GRAPE II processors.
Email: urban@cmm.ki.si
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