The starting point for the method of molecular dynamics (MD) is well defined microscopic description of a physical system consisting of a number of such bodies. Description of the system can be represented in the form of equations of motion of Theoretical Mechanics: Hamiltonian and Lagrangian or express directly by Newton's equations of motion. In the first two cases, the equation of motion must be previously obtained by using the well known formalisms. The method of molecular dynamics, as its name suggests, is used to calculate the property on the basis of the equations of motion, allowing you to get to test the properties of both static and dynamic.
In the molecular dynamics , it is possible to change the temperature in a controlled manner, called a simulated cooling. Apply an alternating sequence of heating and cooling system, so as to finally get frozen in some system configurations (configuration expected to achieve a low-energy).
MD method is based on , the numerical solution of equations of motion using a computer.
Among the many software packages like VEGAZ ZZ, SPARTAN, NANOENGINEER for molecular dynamics deserve a special mention include: Amber, CHARMM, GROMACS, GROMOS, NAMD, Tinker and Desmond.
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