Implementing a new command

ah, that makes sense. I forgot about
the instantaneous approx. Doesn’t this mean
however that in a minimization the force
and energy are not wholly consistent (due
to the contribution to the energy from charge
changes), and thus minimization can stop
early or get confused?


No, the minimization step will not get confused since all fix qeq does before the MD/minimization step is to compute new partial charges on atoms (based on the current position) so that no energy nor force are changed. Fix qeq then supplies the minimizer with new partial charges to compute new energy/forces. If the minimizer decides to stop, then the energy and the force are still consistent.