The three dimensional (3D) structures of bio-molecules such as proteins are important for the development of new drugs. At present, the structures are analyzed as follows. (i) The diffraction patterns of bio-molecules are produced by irradiation of synchrotron radiation xrays onto crystallized bio-molecules. (ii) The structures are reproduced using computer simulations. However, there are a lot of bio-molecules which are very difficult to be crystallized. For such bio-molecules, Neutze et al. proposed that the diffraction patterns are produced from the irradiation of x-rays onto single bio-molecules. Then, the intensity of xrays is required to be very bright. They also suggested that free electron x-ray laser (XFEL) light pulses, which have been developed by US, EU, and Japan, can have enough brightness x-rays (Neutze et al., 2000). When we use single molecules for the analysis of 3D structures, the study of the damage and the destruction of bio-molecules due to the irradiation of XFEL light pulses is indispensable (Hau-Riege et al., 2004, 2007, Jurek et al., 2004, Kai & Moribayashi, 2009, Kai, 2010, Moribayashi & Kai, 2009, Moribayashi, 2008, 2009, 2010, Neutze et al., 2000, Ziaja et al., 2006). We define the damage and the destruction as the ionization and the movement of atoms in a target, respectively (Hau-Riege et al., 2004, Moribayashi, 2008). This comes from the fact that places of the atoms are and are not changed due to the movement and the ionization, respectively. The change of the places means that the reconstruction of the 3D structure cannot be executed. The damage and the destruction mainly occur through the following occurrences: (i) the atoms in the target are ionized through the x-ray absorption or Compton scattering. (ii) From these ionization processes, free electrons, quasi-free electrons and ions are produced and move, where we define ‘a free electron’ and ‘a quasi-free electron’ as an electron, which is ionized from an atom, outside and inside the target, respectively (Hau-Riege et al., 2004, Moribayashi, 2008). (iii) Quasi-free electrons promote the ionization of the other atoms through electron impact ionization processes. (iv) Other ionization processes, such as Auger, also occur. Before experiments of diffraction patterns start, simulations of the damage and the destruction play an important role. The simulations have been executed using various methods, such as molecular dynamics (MD) (Neutze et al., 2000, Jurek et al., 2004), rate equations (Hau-Riege et al., 2004, Hau-Riege et al., 2007, Kai & Moribayashi, 2009, Kai, 2010, Moribayashi, 2008, Moribayashi & Kai, 2009), and kinetic Boltzmann equations (Ziaja et al., 2006). All of these methods have both advantages and disadvantages. In the MD, accurate simulation can be executed for bio-molecules of small size, having up to 10,000 atoms.