Hi I did simulations for a protein with disulfide bonds using opls. Then I reduced the ssbonds in vmd and did simulations for the reduced. When loading gro(or pdb) and trr files on vmd I do not see reduced bonds. I also compared the two pdb files and they looked the same in terms of number of hydrogens in cysteines. So how can I tell if the molecule is properly reduced before going further.
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