Unbiased MD simulations

We have already included the parameters in the SI file, and briefly stated the parameterization in the method section. A more thorough parameterization step is provided as followed, and the gromacs topolgy files are attached: 

For the (FAD)_ox and anionic semiquinone FAD^─●, the force field parameters were adapted from the literature (a  detailed descripition of parameterization documented in I. A. Solov'yov, et al.,. JACS 134, 18046 (2012)), and re-parameterized with CGENFF using CHARMM-GUI to be compatible with the CHARMM36 force fields, this is mainly to resolve some atom type discrepancies between different versions of CHARMM force fields. Finally, CHARMM-GUI provided the gromacs-compatible topology files to faciliate subsequent MD simulation in GROMACS. 

Whereas for the intra-molecular charge transfer state of anionic semiquinone FAD/Ade^─●, we mainly adjusted the partial charges. Specifically, the negative charge distribution on the adenine moiety was obtained by electrostatic potential fitting at the MP2/6-31+G(d) level.  The major differences between the two reduced FAD moieties are in FAD^─●, the flavin ring has an overall -1 charge, whereas the adenine is neutral; in FAD/Ade^─●, the flavin ring is neutral, yet the adenine moiety has an overall -1 charge to mimic the charge transfer process. The VdW parameters and bonding parameters remain the same because the assignment of atom type is preserved for the three forms of FAD cofactor.

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