I am interested in running a system with a combination of fixed and variable charges. The variable charges would be applied to a specified dynamic group of atoms using fix qeq. I plan to figure out the correct parameters, but I just wanted to check if the operation of this fix would work in a mixed fixed/qEq charge system, or if proper operation would require the entire system to have qEq applied.
Yes, it should work. From looking at the source code, the qeq fixes in the QEQ package will only update the charges on atoms in the fix group, but will consider the charges of all neighboring atoms of those atoms. you may have to be careful about the special_bonds settings in case you have bonds in your system. with the default settings, “special” pairs of atoms with a factor of exactly 0.0 will be completely removed from the neighbor list and thus also excluded from the charge equilibration. you need to find out, whether that is consistent with the model you are looking at or not.