What is in silico energy optimization? While doing computational chemistry for both organic and inorganic compounds, an energy optimization of that compound is done before starting a study.

For example, if we do drug docking studies using aspirin, first we would make aspirin's chemical structure, and then we would optimize it. So what does "energy optimization" mean in the context of organic and inorganic compounds.  

Is energy optimization different for organic and inorganic materials (e.g.,aspirin or gold nanoparticles, respectively)?
Generally, energy optimization is done as iterative process with following steps repeating 


calculate forces of nuclei
move nuclei according forces known so final structure were less tense.


Most focus in science is focused on how first step is made, as choice of the second step does not affect final structure except pathological cases. 

The main difference is usually tied to computational capabilities of 'silica' available. Complexity of quantum mechanical computations usually grows as $O(n^3)$, $O(n^4)$ or even $O(e^n)$ where n is number of atoms of same type in system. So, the bigger system is, the 'worse' approximation is used. Biological systems are usually so large, that any sort of quantum mechanical computation is not an option at all, so "molecular mechanics/dynamics" approach is used, with empiric formulas of forces based on relative positions of atoms