Easy creation of polymeric systems for molecular dynamics with Assemble!

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

Research output: Contribution to journalArticlepeer-review

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 a heterogeneous mixture of polybutadiene.
Original languageEnglish
JournalComputer Physics Communications
Early online date18 Jan 2016
DOIs
Publication statusE-pub ahead of print - 18 Jan 2016

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