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)

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