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An explanation of each part displayed in the algorithm is given in the next three parts initialization, production and accumulation. 6.2 INITIALIZATION The initialization procedure is consisting of two steps. The first one is building the simulation box and the second one, calculating the total potential energy of the system. 6.2.1 Solvent Box It is very important, how we are creating the first simulation box. The approach adopted for the determination of the coordinates of the molecules in the box is to start off by placing molecules at random within a box much larger than a box of the target size. The coordinates of atoms are stored in a large Fortran 90 array: ATMCRD (1:3, 1:NATOMS). The size of the large box is then gradually reduced until the target size is reached. The reason for starting off with a large box size is that the probability of having molecules overlap will be small. The initial box length was ten times the target length and the reduction procedure was carried out in ten steps. The number of ten steps has been chosen arbitrary, the more steps the better is but they increase the computational time. After the reduction procedure, the solvent box will have attained the desired volume but the molecules will be by no means fully equilibrated. Thus, the procedure finishes by performing a long Monte Carlo simulation, before writing out the final coordinates to an external file. The coordinates of the last file can be considered as an equilibrated box. Molecular dynamics can be used for the equilibration of the initial box. A different approach is to start all the molecules from a lattice. As moves progress, the lattice “melts” and a simulation box is obtained. The initial period of the simulation is an equilibration period, and must be discarded. We 84PDF Image | MOLECULAR SIMULATION STUDIES IN THE SUPERCRITICAL REGION
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