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Easy creation of polymeric systems for molecular dynamics with Assemble!

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

Easy creation of polymeric systems for molecular dynamics with Assemble! Thumbnail


Authors

V. Erastova



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.

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.
Public URL https://durham-repository.worktribe.com/output/1420719

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