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know that the final result should be independent of the starting configuration, so we checked this by checking the results with using different initial boxes. As pointed out before, the choice of number of molecules is crucial for the calculation of any thermodynamic property. We choose to use 1000 solvent molecules as a solvent box. The number 1000 is chosen as it is sufficient to describe the system and efficient for keeping down the computational time. Furthermore, other research groups use relevant amount of particles at similar conditions (Song and Maroncelli, 2003). 6.2.2 Potential Energy The calculation of the potential energy is crucial for the Monte Carlo procedure. As we mentioned in the previous chapter, the energy is calculating by adding the energy of pairs of particles. If intermolecular interaction is restricted to pairs of N molecules, the total potential energy is obtained by summing over the contribution all of the individual pairs. A pseudo-code scheme for the calculating the total energy is given below: loop i 1 ... N loop j 1 ... i-1 Evaluate rij. Evaluate u(rij). Accumulate energy. end j loop end i loop The above pseudo code illustrates the nesting of loops required for the Naïve evaluation of energy by equation (5.1). If there are N molecules in the simulation, then to calculate the pairwise energy experienced by each other molecule involves a 85PDF Image | MOLECULAR SIMULATION STUDIES IN THE SUPERCRITICAL REGION
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