Molecular dynamics simulation of a polymer chain in solution by collisional dynamics method

This article describes the collisional dynamics (CD) method adapted for molecules with geometrical constraints within a description using Cartesian coordinates for the atoms. In the CD method, stochastic collisions with virtual particles are included in usual molecular dynamics simulations to couple the considered polymer molecule to a solvent. The actual presence of the solvent is not explicitly included in the simulation. The results-of CD simulations of a polymer chain immersed in the time-dependent elongational flow field are presented. The influence of nonbonded interactions on the coil-stretch transition of the chain occurring in the flow is discussed.