Markov model-based polymer assembly from force field-parameterized building blocks.

Durmaz, Vedat

A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very work-intensive and time-consuming. Using the example of polyglycerol, I present a polymer decompostion strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantum-chemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers.

MARKOV processes; MOLECULAR self-assembly; MOLECULAR force constants; ELECTROSTATICS; NUCLEOTIDE sequence; MOLECULAR dynamics

Journal of Computer-Aided Molecular Design, 2015, Vol 29, Issue 3, p225

0920-654X

Academic Journal

10.1007/s10822-014-9817-0