General Equation of Motion

The equations of motion, generalized to include holonomic or nonholonomic constraints with Lagrange multipliers, are... 

All chemical process involves the motion of atoms within a molecule. Molecular dynamics (MD), in the broadest sense, is concerned with molecules in motion. It combines the energy calculations from molecular mechanics with equations of motion. Generally, an appropriate starting structure is selected (normally an energy minimized structure). Each atom in the system is then assigned a random velocity that is consistent with the Maxwell-Boltzmann distribution for the temperature of interest. The MM formalism is used to calculate the forces on all the atoms. Once the atom positions are known, the forces, velocities at time t, and the position of the atoms at some new time t + 5t can be predicted. More details about the method can be found in Ref.. ... 

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