Atomistic-to-continuum coupling methods are used to unravel molecular mechanisms of polymers and polymer composites. These multiscale techniques advantageously combine the computational efficiency of continuum approaches while keeping the accuracy of particle-based methods. The Capriccio method [Pfaller et al. Comput. Methods Appl. Mech. Eng. 2013, 260, 109-129.] is a well-proven multiscale technique, which connects finite elements (FE) with molecular dynamics (MD) in a partitioned-domain approach. A vital aspect of these multiscale methods is to provide physically sound boundary conditions to the particle domain suppressing any interface effects at the domain boundary occurring due to the coupling. These interfacial coupling artifacts still pose a significant problem, especially for amorphous polymers due to their highly irregular microstructure. We solve this problem by extending the particle-continuum interface by a layer of passive atoms which move with the outer continuum, thereby providing the missing interactions with a surrounding polymer bulk to the inner particle region. This solution allows us to successfully reproduce structural and mechanical properties obtained under conventional periodic boundary conditions, like density, stress, Young's modulus, and Poisson's ratio. Furthermore, we demonstrate the application of a nonaffine deformation by means of a simple bending test. In general, our revised method provides a framework to apply complex deformations for molecular scientists, while it allows the engineering community to examine challenging phenomena such as fracture behavior at a molecular level.