Open Access

ARTICLE

A Geometric Embedding Algorithm for Efficiently Generating Semiflexible Chains in the Molten State

M. Kröger¹, M. Müller², J. Nievergelt²

1 Institute of Theoretical Physics, University of California Santa Barbara, USA, and Polymer Physics, ETH Zürich, Switzerland, and Institute of Theoretical Physics, TU Berlin, Germany. Email: editors@AR.ethz.ch
2 Department of Computer Science, Institute of Theoretical Computer Science, ETH Zürich, Switzerland

Computer Modeling in Engineering & Sciences 2003, 4(5), 559-570. https://doi.org/10.3970/cmes.2003.004.559

Abstract

We present a novel method for generating starting polymer structures for molecular simulations in the dense phase. The work describes the ingredients of an algorithm for the creation of large, dense or diluted amorphous polymeric systems close to equilibrium and provides measures for its quality. The model systems are made of semiflexible (wormlike) repulsive multibead chains. The key feature of the method is its efficiency, in particular for large systems, while approaching given local and global chain characteristics. Its output has been proven to serve as an excellent basis for subsequent off-lattice molecular dynamics computer simulation. By combining chain growing with an iterative relaxation technique we remove overlaps of monomers. The computing time is linear in the number of beads and independent of chain length. The method succeeds in generating large and dense (bulky and confined) systems of up to$100,000$ beads in less than an hour on todays workstations.

---

Keywords

---