Easy creation of polymeric systems for molecular dynamics with Assemble!

Degiacomi, M.T.; Erastova, V.; Wilson, M.R.

Abstract

We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with Gromacs. We illustrate the capabilities of Assemble! by demonstrating the easy preparation of a 300 monomers-long polyisoprene in hexane, and an heterogeneous mixture of polybutadiene.

Citation

Degiacomi, M., Erastova, V., & Wilson, M. (2016). Easy creation of polymeric systems for molecular dynamics with Assemble!. Computer Physics Communications, 202, 304-309. https://doi.org/10.1016/j.cpc.2015.12.026

• Journal Article Type: Article
• Acceptance Date: Dec 13, 2015
• Online Publication Date: Jan 18, 2016
• Publication Date: May 1, 2016
• Deposit Date: Feb 4, 2016
• Publicly Available Date: Jan 18, 2017
• Journal: Computer Physics Communications
• Print ISSN: 0010-4655
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 202
• Pages: 304-309
• DOI: https://doi.org/10.1016/j.cpc.2015.12.026
• Keywords: Polymeric mixture, Molecular dynamics, Gromacs, Simulation preparation.