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Some initial configurations were performed in the initial setup phase before the study commenced.
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A thermal optimization of the configuration is performed to compare the changes observed between initial and optimized design.
In addition, data rate configuration is performed at the sender.
Then, routing configuration is performed to make the MN accessible.
In the experiments more initial configurations were tested.
In each run, Ninit = 10 random initial configurations are generated, and only the best Ninit _ locsch = 10 initial configurations were selected for the steepest-descent search.
After generating Ninit = 1000 random initial configurations, only the best Ninit _ locsch = 100 initial configurations were selected for the steepest-descent search.
For the gmfit program, of the Ninit = 1000 random initial configurations generated, only the best Ninit _ locsch = 100 initial configurations were selected for the steepest-descent search with symmetric restraints.
The initial configurations were energy minimized using the steepest descent algorithm for 1000 steps to remove any unexpected coordinate collisions.
Initial configurations were subjected to a 500-step minimization with the harmonic constraints of 10 kcal⋅mon−1⋅Å−2 on the protein heavy atoms.
To find the lowest-energy configuration, many initial configurations are randomly generated, and the steepest-descent local search is performed for each of them.
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