  We describe a method to compute photon-matter interaction and atomic dynamics
with X-ray lasers using a hybrid code based on classical molecular dynamics and
collisional-radiative calculations. The forces between the atoms are
dynamically computed based on changes to their electronic occupations and the
free electron cloud created due to the irradiation of photons in the X-ray
spectrum. The rapid transition from neutral solid matter to dense plasma phase
allows the use of screened potentials, which reduces the number of non-bonded
interactions required to compute. In combination with parallelisation through
domain decomposition, large-scale molecular dynamics and ionisation induced by
X-ray lasers can be followed. This method is applicable for large enough
samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that
when exposed to an X-ray laser pulse turn into a plasma in the first few
femtoseconds of the interaction. We show several examples of the applicability
of the method and we quantify the sizes that the method is suitable for. For
large systems, we investigate non-thermal heating and scattering of bulk water,
which we compare to previous experiments. We simulate molecular dynamics of a
protein crystal induced by an X-ray pump, X-ray probe scheme, and find good
agreement of the damage dynamics with experiments. For single particle imaging,
we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond
X-ray laser. In the context of coherent diffractive imaging we study the
fragmentation as given by an X-ray pump X-ray probe setup to understand the
evolution of radiation damage.
