Figure 9 Pseudo Algorithm for Initialization  (Adapted from D. Frenkel and B. Smit, Understanding Molecular Simulation, From Algorithms to Applications, 2nd ed., Academic Press, London, 2001.)

PACKMOL is an excellent package which initializes the positions of the particles. It creates an system by packing molecules in defined regions of space. This packing guarantees that short range repulsive interactions do not disrupt the simulations. It can handle variety of spatial constraints which are attributed to the molecules, or atoms within the molecules. This makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers. Here the user provides the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy. The details can be found from the following link: http://www.ime.unicamp.br/~martinez/packmol/

The Force Calculation
For a model system of N molecules we consider pairwise additive interactions. Considering the interaction between a particle and the nearest image of another particle we have have to compute N×(N-1)/2 pair distances.So the force calculation is the most expensive in the MD simulation.There exits number of methods that reduces the evaluation of both short and long range forces in such a way that the time scales as N instead of N². We however display a simple algorithm for the force calculation

Figure 10 Force calculation in MD  (Adapted from D. Frenkel and B. Smit, Understanding Molecular Simulation, From Algorithms to Applications, 2nd ed., Academic Press, London, 2001.)