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We carried out the minimization using the local minimizer 'lsqnonlin' function of Matlab [ 27, 28].
All the resulting structures were energy minimized with a standard 100 ABNR steps minimization using the software CHARMm [26], and charmm19 parameters.
The crystal structure of the hAR obtained from the Protein Data Bank entry 1e3g (PDB 2009) was subjected to minimization using the Amber99 force field embedded in MOE, and the minimized structure was used as template for dockings with all ligands.
The models were optimized by potential energy minimization using the SYBYL ® software package.
All systems were first subjected to potential energy minimization using the steepest descent algorithm and then to solvent equilibration (50 ps) in the canonical (NVT) ensemble at 298 K.
Recently, research on entropy generation minimization using the second law of thermodynamics has been studied for many different situations.
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The energy minimization used the default method of AMBER 5.0 (10 cycles of the steepest descent method followed by the conjugate gradient method).
Energy minimization used the steepest descent method for 5000 steps.
The minimization used the steepest descent method for 5,000 steps before transferring the final structure to MD simulation.
The minimization used the steepest descent method for 5,000 steps; then the final structure with the lowest energy was transferred to MD simulation.
Three initial configurations were subjected to energy minimizations using the same methodology described above for the inorganic and organic U-complexes.
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