MD simulation ATOMS

In MD simulation, atoms and molecules are allowed to interact for a period of time by approximations of known physics in order to explore the physicochemical properties of solutions and structures such as interfacial phenomena and the dynamics of water molecules and ions, thus providing detailed information and fundamental understanding on relationships between molecular structure, movement, and function (Brossard et al. 2008 Du and Miller 2007a, 2007b Du et al. 2007a, 2007b Lazarevic et al. 2007 Miller et al. 2007 Nalaskowski, et al. 2007). With MD simulation, scientists are able to examine the motion of individual atoms and molecules in a way not possible in laboratory experiments. 

In molecular dynamics (MD) simulation atoms are moved in space along their lines of force (which are determined from the first derivative of the potential energy function) using finite difference methods [27, 28]. At each time step the evolution of the energy and forces allow the accelerations on each atom to be determined, in turn allowing the atom changes in velocities and positions to be evaluated and hence allows the system clock to move forward, typically in time steps of the order of a few fs. Bulk system properties such as temperature and pressure are easily determined from the atom positions and velocities. As a result simulations can be readily performed at constant temperature and volume (NVT ensemble) or constant temperature and pressure (NpT ensemble). The constant temperature and pressure constraints can be imposed using thermostats and barostat [29-31] in which additional variables are coupled to the system which act to modify the equations of motion. 

In reality, atoms and molecules in solid materials are far from static unless the temperature is low but even at 0 K, vibrational motion remains. For ionically conductive materials, atomic movement is the subject of major interest. allows us to simulate the dynamics of the particles in a well-defined system to gain greater insights into local structure and local dynamics - such as ion transport in solid materials. In an MD simulation, atomic motion in a chemical system is described in classical mechanics terms by solving Newton s equations of motion ... 

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