====== MD simulations Restrained by X-ray Diffraction Data ======
====== Outline ======
  * Run phenix.fmodel to calculate structure factor of 3ONS (Solvent is ignored). Write a python code to calculate structure factor and make sure we get the same result. The python code will have two versions (the two versions should give the same result):
    *. Perform symmetry operators to build a complete unitcell, and then calculate SF by assuming no mirror molecules
    *. Do not expand the symmetry. Calculate SF under proper symmetry operators (use Seitz matrices as Phenix does)

  * Write a Fortran code by using Oleg's code as a template.

  * Integrate the code into Amber's minimization function, and observe the convergence

  * If minimization works well, then integrate the code into Amber's dynamics function