By Akira Satoh
This booklet offers crucial and major thoughts of the molecular and microsimulation options. It enables readers to enhance their talents for constructing simulation courses by way of supplying actual difficulties and pattern simulation courses for them to use.Provides instruments to improve talents in constructing simulations programsIncludes pattern simulation courses for the reader to useAppendix explains Fortran and C languages purely to permit the non-expert to exploit them
Read or Download Introduction to Practice of Molecular Simulation: Molecular Dynamics, Monte Carlo, Brownian Dynamics, Lattice Boltzmann and Dissipative Particle Dynamics (Elsevier Insights) PDF
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Extra info for Introduction to Practice of Molecular Simulation: Molecular Dynamics, Monte Carlo, Brownian Dynamics, Lattice Boltzmann and Dissipative Particle Dynamics (Elsevier Insights)
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13, a particle crossing and exiting the left boundary surface has to enter from the right virtual box. 13 Periodic boundary condition. The rounding-up function DNINT can yield a simple one-line expression as RXI5RXI2DNINT(RXI/LX)*LX Note that the position of particle i is denoted by (RXI, RYI). Similar procedures have to be conducted for the case of the y- and z-directions. When the interaction energy or force of particle i with other particles, for example, particle j, is calculated, an appropriate particle j has to be chosen as an object from real and virtual particles j.
In addition, the x-component vx of these particles needs to be modified to (vx 2 U), but the y-component vy can be used without modification. 14 Simple shear flow. 15 LeesÀEdwards boundary condition. The y- and z-coordinates are treated as in the periodic boundary condition, and the modification of vy and vz is unnecessary. For the case of evaluating interaction energies or forces, the similar procedures have to be conducted for the particles interacting with virtual particles which are in the replicated simulation boxes in the upper or lower layers.
3), the force fqp exerted by molecule p on molecule q can be derived as ( 6 ) σ 12 σ rqp 2 f qp 5 24ε 2 2 rqp rqp rqp ð3:4Þ Practice of Molecular Dynamics Simulations 51 in which rqp is the relative position vector of molecule q to molecule p, expressed as rqp 5 rq 2 rp, and rqp 5 jrqpj. In practice, simulations usually treat a nondimensional system, in which the governing equations and all physical quantities are nondimensionalized by certain representative values. Therefore, in the following paragraphs, we show the method of nondimensionalizing the equations.