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The model was minimized according to our recent papers [29].

The model was minimized by 2000 steps of steepest descent and 1000 steps of conjugate gradient and then equilibrated at the desired temperature and pressure for 50 ps, with all atom restraints except hydrogens, followed by 1 ns free of any atomic restraints.

Finally, the model was minimized using GROMACS [ 97, 98] and its stereochemical quality was evaluated using PROCHECK [ 99].

The goal of the model was minimizing transportation time and it was formulated as a MILP and solved by Tabu search for large instances.

The multi-objectives of the model are minimizing the average distribution time and the distribution time of the slowest channel.

Finally the models were minimized without constraints.

The models were minimized by 1000 conjugate gradient steps for equilibration, heated from 2 K to 300 K during 35 psec at temperature increment of 50 K per 5 psec, then the constant temperature and pressure algorithm was applied at 300 K for 200 psec.

The objective function of this model was minimizing the external and internal transportation costs and holding costs of inventory in distribution centers.

The final model was minimized again using the ROSETTA relax-fast protocol [ 77] and its quality evaluated.

In each simulation, the initial model was minimized in order to reduce the contact area difference (CAD) between the protein model and the solvent molecule.

The final model was minimized using SYBYL package (SYBYL7.1, Tripos Inc) with the following parameters: Tripos force field, 1000 iterations using Powell's gradient and was terminated at a convergence of 0.05 Kcal mol Å−1.