A brownian dynamics simulation method has been implemented to study the superoxide-superoxide dismutase association reaction. Starting from electrostatic potential and forces calculated by solving the linearized finite difference Poisson-Boltzmann equation brownian dynamics trajectories are simulated to compute the diffusion contribution, which is known to be the dominant one, to the catalytic rate. The algorithm has been tested carrying out simulations at different ionic strength values on bovine Cu,Zn superoxide dismutase (SOD). A completely parallel code has been developed using PVM. Parallellization has been implemented using a dynamical strategy to ensure maximum performance over non-dedicated parallel computer with distributed sources. The software has been developed over a IBM-R6000 RISC cluster, using PVM 3.3.x version.
Brownian Dynamics Simulation of Diffusion Controlled Reactions. A Parallel Approach Using PVM on a RISC-Cluster
FIUMARA, Giacomo;SERGI, ALESSANDRO;CARISTI, Giuseppe;FERRARIO, Mauro;DESIDERI, Alessandro
1994-01-01
Abstract
A brownian dynamics simulation method has been implemented to study the superoxide-superoxide dismutase association reaction. Starting from electrostatic potential and forces calculated by solving the linearized finite difference Poisson-Boltzmann equation brownian dynamics trajectories are simulated to compute the diffusion contribution, which is known to be the dominant one, to the catalytic rate. The algorithm has been tested carrying out simulations at different ionic strength values on bovine Cu,Zn superoxide dismutase (SOD). A completely parallel code has been developed using PVM. Parallellization has been implemented using a dynamical strategy to ensure maximum performance over non-dedicated parallel computer with distributed sources. The software has been developed over a IBM-R6000 RISC cluster, using PVM 3.3.x version.Pubblicazioni consigliate
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