  The accurate description of large molecular systems in complex environments
remains an ongoing challenge for the field of computational chemistry. This
problem is even more pronounced for photo-induced processes, as multiple
excited electronic states and their corresponding non-adiabatic couplings must
be taken into account. Multiscale approaches such as hybrid quantum
mechanics/molecular mechanics (QM/MM) offer a balanced compromise between
accuracy and computational burden. Here, we introduce an open-source software
package (INAQS) for non-adiabatic QM/MM simulations that bridges the sampling
capabilities of the GROMACS MD package and the excited-state infrastructure of
the Q-CHEM electronic structure software. The interface is simple and can be
adapted easily to other MD codes. The code supports a variety of different
trajectory based molecular dynamics, ranging from Born-Oppenheimer to surface
hopping dynamics. To illustrate the power of this combination, we simulate
electronic absorption spectra, free energy surfaces along a reaction
coordinate, and the excited state dynamics of 1,3-cyclohexadiene in solution.
