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Easy creation of polymeric systems for molecular dynamics with Assemble!

Degiacomi, Matteo T. and Erastova, Valentina and Wilson, Mark R. (2016) 'Easy creation of polymeric systems for molecular dynamics with Assemble!', Computer physics communications., 202 . pp. 304-309.

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.

Item Type:Article
Keywords:Polymeric mixture, Molecular dynamics, Gromacs, Simulation preparation.
Full text:(AM) Accepted Manuscript
Available under License - Creative Commons Attribution Non-commercial No Derivatives.
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Status:Peer-reviewed
Publisher Web site:http://dx.doi.org/10.1016/j.cpc.2015.12.026
Publisher statement:© 2016 This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
Date accepted:13 December 2015
Date deposited:05 February 2016
Date of first online publication:18 January 2016
Date first made open access:18 January 2017

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