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Department of Earth Sciences

Academic Staff

Publication details for Dr Valentina Erastova

Degiacomi, M.T., Erastova, V. & Wilson, M.R. (2016). Easy creation of polymeric systems for molecular dynamics with Assemble! Computer Physics Communications 202: 304-309.

Author(s) from Durham

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.