Periodic boundaries

Periodic boundary conditions force k to be a discrete variable with allowed values occurring at intervals of lull. For very large systems, one can describe the system as continuous in the limit of i qo. Electron states can be defined by a density of states defmed as follows ... 

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.

Felderhof B U 1980 Fluctuation theorems for dielectrics with periodic boundary conditions Physice A 101 275-82... 

Figure 3. Floquet band structure for a threefold cyclic barrier (a) in the plane wave case after using Eq. (A.l 1) to fold the band onto the interval —I < and (b) in the presence of a threefold potential barrier. Open circles in case (b) mark the eigenvalues at = 0, 1, consistent with periodic boundary conditions. Closed circles mark those at consistent with sign-changing...

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). 

Wood, R.H. Continuum electrostatics in a computational universe with finite cut-off radii and periodic boundary conditions Correction to computed free energies of ionic solvation. J. Chem. Phys. 103 (1995) 6177-6187. 

Very recently, we have developed and incorporated into the CHARMM molecular mechanics program a version of LN that uses direct-force evaluation, rather than linearization, for the fast-force components [91]. The scheme can be used in combination with SHAKE (e.g., for freezing bond lengths) and with periodic boundary conditions. Results for solvated protein and nucleic-... 

There are three different algorithms for the calculation of the electrostatic forces in systems with periodic boundary conditions (a) the (optimized) Ewald method, which scales like (b) the Particle Mesh... 

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.

The problems already mentioned at the solvent/vacuum boundary, which always exists regardless of the size of the box of water molecules, led to the definition of so-called periodic boundaries. They can be compared with the unit cell definition of a crystalline system. The unit cell also forms an "endless system without boundaries" when repeated in the three directions of space. Unfortunately, when simulating hquids the situation is not as simple as for a regular crystal, because molecules can diffuse and are in principle able to leave the unit cell. 

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. 

Often yon need to add solvent molecules to a solute before running a molecular dynamics simiilatmn (see also Solvation and Periodic Boundary Conditions" on page 62). In HyperChem, choose Periodic Box on the Setup m en ii to enclose a soln te in a periodic box filled appropriately with TIP3P models of water inole-cii les. 

Note MM-i- is derived from the public domain code developed by Dr. Norm an Allinger, referred to as M.M2( 1977), and distributed by the Quantum Chemistry Program Exchange (QCPE). The code for MM-t is not derived from Dr. Allin ger s present version of code, which IS trademarked MM2 . Specifically. QCMPOlO was used as a starting point Ibr HyperChem MM-t code. The code was extensively modified and extended over several years to include molecular dynamics, switching functuins for cubic stretch terms, periodic boundary conditions, superimposed restraints, a default (additional) parameter scheme, and so on. 

Hor the periodic boundary conditions described below, the ctitoff distance is fixed by the nearest image approximation to be less than h alf th e sm allest box len gth. W ith a cutoff an y larger, more than nearest images would be included. 

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. 

It is also possible to simulate liquid droplets by surrouridiu g a solute by a fin ite ii urn ber of water moleeu les an d perform in g the sim -ulalion without a periodic box. The water, of course, eventually evaporates and moves away from the solute when periodic boundary con ditioii s arc n ot im posed. If the water is in itially added via periodic boundary con dition s, you rn ust edit the resu Itin g H IN file to remove th e periodic boti ruiary con ditioii s, if a droplet approach is desired. 

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. 

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