Application of the Monte Carlo method for creation of initial models of EAP molecules for Molecular Dynamics simulation

摘要

A program called mcgen was written for creating initial models for Molecular Dynamics simulations with capability to arrange at least the following into simulation cell: branched and non-branched polymers, copolymers, nanoparticles, dissolved salts (ions), liquids. The program was tested with non-branched poly(ethylene oxide) molecules and the optimal values were found for the control parameters the Monte Carlo algorithm depends on, such that the program works steady and fast enough. Generation features of mcgen allow to generate one or several chains of the same or different types; add side-chains with fixed or random spacing along the main chain; insert atoms and ions into the simulation cell before generating the polymers; mark given atoms as "invisible" so that those atoms are not checked against any geometric constraints and will be removed from the simulation cell, if they happen to be on the way of the growing polymer chain; establish geometric constraints (sphere, upper and/or lower limit on one, two or all three axes) and generate polymer chains either inside or outside them.