Molecular dynamics simulation of simple polymer chain formation using divide and conquer algorithm based on the augmented Lagrangian method

Abstract

This paper presents an efficient multibody methodology for the simulation of molecular dynamics of simple polymer chains. The algorithm is formulated in terms of absolute coordinates. The augmented Lagrangian method is incorporated into the divide and conquer framework giving new parallel, logarithmic order algorithm suitable for the simulation of general multibody system topologies. The approach is robust in case of potential rank deficiencies of the Jacobian matrices that embrace the group of systems involving redundant constraints, and which may repeatedly enter singular configurations. Series of nanosecond-long molecular dynamics simulations of simplified polymer chain models are performed to demonstrate the correctness of the methodology and investigate the structure formation of the system subjected to non-bonded (Lennard-Jones) and bonded (torsional) interactions. Conformational changes and dynamic properties of the polymer chains are studied under gradual cooling of the system. The simulation results show that some of the homopolymers collapse into well-formed helices. The fraction of the succeeded runs, in which defect-free helices are found, is a function of initial conditions, chain length, and cooling rate. The employed computational multibody approach appeared to be useful in molecular dynamics simulations implying potential for future research and further development in this field.

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