A new method to build an initial configuration for molecular modeling.

CONTEXT: Generally, the initial structures of large simulated systems containing discoid, tree-like, fiber-like etc. molecules obtained using conventional methods have very low density. So, their compression to target values is a special stage of data preparation, performed by multi-step protocols that require a lot of calendar and computer time. A new method for generating initial configurations of large-scale molecular models is presented, using the concept of "parallel 4D universes" to densely pack components into the basic cell of the simulated system. Examples of constructing simulated systems containing millions of atoms are given.

METHODS: Monte Carlo simulations were performed using Metropolis sampling procedure for NVT ensemble. A software package was developed by author implementing a domain decomposition strategy to speed up the calculations. Short-range atom-atom potential functions were used to model van der Waals and electrostatic interactions as well as quadratic potential to incorporate the covalent bonds/angles deformation energy and the penalty functions to separate overlapping molecular fragments.