Periodic Boundary Condition Simulations

Computer simulations of bulk liquids are usually performed by employing periodic boundary conditions in all three directions of space, in order to eliminate artificial surface effects due to the small number of molecules. Most simulations of interfaces employ parallel planar interfaces. In such simulations, periodic boundary conditions in three dimensions can still be used. The two phases of interest occupy different parts of the simulation cell and two equivalent interfaces are formed. The simulation cell consists of an infinite stack of alternating phases. Care needs to be taken that the two phases are thick enough to allow the neglect of interaction between an interface and its images. An alternative is to use periodic boundary conditions in two dimensions only. The first approach allows the use of readily available programs for three-dimensional lattice sums if, for typical systems, the distance between equivalent interfaces is at least equal to three to five times the width of the cell parallel to the interfaces. The second approach prevents possible interactions between interfaces and their periodic images. 

Fig. 6. Visulization of the Monte Carlo simulation periodic boundary conditions are used where the mirror image of a particle enters through the opposite face when a particle leaves (Ref. 24).

To avoid potential water-vacuum interface problems that might arise in a MD simulation, periodic boundary conditions arc commonly used." Basically, a protein is surrounded by a rectangular hox of water with a defined number of water structures. This water box is then surrounded un each face by another water box. When the MD simulation is being carried out. water near the edges of the central box containing the protein may leave and be replaced with a water coming from the water box on the opposite side. This procedure ensures that the waters inside the central water box remain constant. 

When we solve the problem numerically, the number of surface elements, and consequently, the size of the dielectric boundary surfaces must be finite. This is in accordance with the practice in a simulation, where the simulation cell is also finite. To approximate an infinite system in a simulation, periodic boundary conditions are applied in the x and y directions. The closest image convention is used not only for the ionic distances but any distances between... 

In order to avoid siuface effects for condensed phase simulations, periodic boundary conditions are applied. The central computational box is replicated infinitely in all dimensions. A detailed description can be found in the textbooks of Allen and Tildesley [10] as well as of Frenkel and Smit [11],... 

For the micro-scale simulations of flow around textile fibers, Sobera et al. [8] simulated a 3-dimensional flow domain, with a virtual textile plane halfway and parallel to the inflow and outflow boundary of the domain. The inflow boundary conditions (laminarized flow in the vicinity of the textile) are obtained from the meso-scale DNS simulations. Periodic boundary conditions are applied to the edges of the virtual textile. Considering the textile as a 2-dimensional array of cylinders, at a mutual half distance, porosity is given by ... 

The alternative simulation approaches are based on molecular dynamics calculations. This is conceptually simpler that the Monte Carlo method the equations of motion are solved for a system of A molecules, and periodic boundary conditions are again imposed. This method pennits both the equilibrium and transport properties of the system to be evaluated, essentially by numerically solvmg the equations of motion... 

Figure B3.3.3. Periodic boundary conditions. As a particle moves out of the simulation box, an image particle moves in to replace it. In calculating particle interactions within the cutoff range, both real and image neighbours are included.

If the simulated system uses periodic boundary conditions, the logical long-range interaction includes a lattice sum over all particles with all their images. Apart from some obvious and resolvable corrections for self-energy and for image interaction between excluded pairs, the question has been raised if one really wishes to enhance the effect of the artificial boundary conditions by including lattice sums. The effect of the periodic conditions should at least be evaluated by simulation with different box sizes or by continuum corrections, if applicable (see below). 

Fig. 1. Periodic boundary conditions protect the inner simulation cell from disturbing effects of having all its particles close to the surface. With PBCs in force, as a particle moves out of the box on one side, one of its images will move back into the box on the opposite side.

A typical molecular dynamics simulation comprises an equflibration and a production phase. The former is necessary, as the name imphes, to ensure that the system is in equilibrium before data acquisition starts. It is useful to check the time evolution of several simulation parameters such as temperature (which is directly connected to the kinetic energy), potential energy, total energy, density (when periodic boundary conditions with constant pressure are apphed), and their root-mean-square deviations. Having these and other variables constant at the end of the equilibration phase is the prerequisite for the statistically meaningful sampling of data in the following production phase. 

Isolated gas ph ase molecules are th e sim plest to treat com pii tation -ally. Much, if not most, ch emistry lakes place in the liq iiid or solid state, however. To treat these condensed phases, you must simulate continnons, constant density, macroscopic conditions. The usual approach is to invoke periodic boundary conditions. These simulate a large system (order of 10" inoleeti les) as a contiruiotis replication in all direction s of a sm nII box, On ly th e m olceti Ics in the single small box are simulated and the other boxes arc just copies of the single box. 

Periodic boundary conditions can also be used to simulate solid state con dition s although TlyperChem has few specific tools to assist in setting up specific crystal symmetry space groups. The group operation s In vert, Reflect, and Rotate can, however, be used to set up a unit cell manually, provided it is rectangular. 

For some simulations it is inappropriate to use standard periodic boundary conditions in all directions. For example, when studying the adsorption of molecules onto a surface, it is clearly inappropriate to use the usual periodic boundary conditions for motion perpendicular to the surface. Rather, the surface is modelled as a true boundary, for example by e, plicitly including the atoms in the surface. The opposite side of the box must still be treated when a molecule strays out of the top side of the box it is reflected back into the simulation cell, as indicated in Figure 6.6. Usual periodic boundary conditions apply to motion parallel to the surface. 

The first molecular dynamics simulations of a lipid bilayer which used an explicit representation of all the molecules was performed by van der Ploeg and Berendsen in 1982 [van dei Ploeg and Berendsen 1982]. Their simulation contained 32 decanoate molecules arranged in two layers of sixteen molecules each. Periodic boundary conditions were employed and a xmited atom force potential was used to model the interactions. The head groups were restrained using a harmonic potential of the form ... 

It is sometimes desirable to include the effect of the rest of the system, outside of the QM and MM regions. One way to do this is using periodic boundary conditions, as is done in liquid-state simulations. Some researchers have defined a potential that is intended to reproduce the effect of the bulk solvent. This solvent potential may be defined just for this type of calculation, or it may be a continuum solvation model as described in the next chapter. For solids, a set of point charges, called a Madelung potential, is often used. 

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