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Biophisics

EQUILIBRATION. This is the act of maintaining or bringing into equilibrium It brings about a balanced relationbetween theories and experimental results. For equilibrium to be reached simulation method is used. This is necessary because it may be difficult or impossible to test certain factors .e.g. Extreme temperatures and pressures. The equilibrium cannot be reached. Another way to reach equilibrium is by generating initial methods using the Monte Carlo (MD) method.Physical properties of molecular dynamics simulation.Quantities fluctuate around average values. Average should remain constant overtime (no systematic shift). Different initial conditions (spatial coordinates and velocities) should produce the same thermodynamic quantities after equilibrium. Scaling velocities as occasionally to reach the desired temperature and during data collection to maintain correct ensemble. The equilibrium state is micro canonical at given total energy. For example, (E tot= E pot+ E kin).Generate initial velocities for specified temperature. To ensure full temperatures generate initial velocities.These quantities are. Potential energy (Pot).This property should change in a systematic fashion and fluctuate along mean values.Kinetic energy (Kin).Should be greater than zero. (E kin gt. 0).The lattice initialization procedure outlined cannot reach all possible values of energy.ie. (E totgt. E pot (lattice)).Work cited.Molecular dynamics: Classical to Quantum methods, Perla Balbuena, Jorge. M. Seminario, 1999.V. May and O. Kuhn, Charge and Energy Transfer in Molecular Systems, 3rd edition (Wiley VCH, 2011).Alder, B.J. T.E, Wainwrights (1959): studies in Molecular Dynamics 1.D.C.RAPAPORT: The Art of Molecular Dynamics Simulation, 2rd edition, 2004.

Biophisics