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Molecular Dynamics

Dynamics methods approximate the movements of atoms. The potential energy of a molecular system is governed by the empirical force field. The Scigress computational application Dynamics uses the same force fields as the Mechanics application. The kinetic energy of a molecular system is derived from the atomic velocities, which in turn are chosen to reflect the temperature of the simulation. By executing Dynamics simulations, you can observe the molecular systems that you are studying in motion.

While Mechanics methods can produce low-energy conformations for molecular systems, they offer no information about the motions of the atoms. A molecular dynamics trajectory approximates the real motions in a molecular system by using the same force field equations that describe the potential energy of a molecule in terms of molecular geometries to evaluate the forces on each atom.

By integrating Newton's equation of motion, atomic velocities can be obtained from the forces on each atom. For any given temperature, an initial set of velocities can be selected from the Maxwell-Boltzmann distribution and a trajectory through time can be generated for any molecular system.

The Scigress Dynamics program uses the same force fields as the Scigress Mechanics program, and it utilizes the Verlet algorithm to update the velocities. The Verlet algorithm is a second order numerical integration of Newton's equation of motion. This dynamics simulation conserves the total (potential plus kinetic) energy, and the volume of the entire system. This type of simulation is also known as a microcanonical ensemble at temperature T.

Scigress Dynamics generates a trajectory according to the settings that you specify. A trajectory is a collection of structures arranged sequentially in time. Each structure has a potential and a kinetic energy associated with it, as well as a temperature. You can examine the energies and the related structures simultaneously in two side-by-side windows by opening the map file dynamics.map, which is created when you perform an experiment in Dynamics. Generating trajectories can give you information about:

  • The various conformations that occur as a result of normal molecular motion.

  • The structure-energy relationships of the molecule.

  • Regions of the conformational space occupied by the system when applying a high temperature, and therefore a large amount of kinetic energy, to give the molecule enough energy to escape a local energy minimum.