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The simulation systems were first energy minimised by using the steepest descent method.
Each system was energy minimized by using the steepest descent method to relax any steric conflicts before beginning the simulations.
Energy minimization for each structure was performed by using the steepest descent algorithm with an initial step size 0.02 nm.
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The UNANR model does not contain a bias unit, and the coefficients are adaptively updated by using the steepest-descent algorithm.
Hydrogen atoms were added and the molecule was energy minimized using CHARMM program [27] and the force field PARAM22 [28] by using the steepest-descent algorithm.
The juice yield was optimized further in a new experimental template, made by using the statistical steepest ascent optimization method.
All the structures were built using the Avogadro package [56], and then the optimized structures were obtained by first relaxing the structures using the Steepest Descent algorithm in the Avogadro, without any symmetry constraints.
The reconstruction is realized by the minimization of a cost function using the steepest descent method.
Each system was minimized for 500 steps using the steepest descent algorithm followed by 500 steps with the conjugate gradient algorithm.
An initial conformation was produced by minimising the energy of the system for 1000 steps using the steepest descents algorithm.
Energy minimization was performed using the steepest decent algorithm for 2000 steps followed by position-restraint dynamics (5 ns in length) restraining the protein to the initial coordinates.
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