Easy creation of polymeric systems for molecular dynamics with Assemble!
MT Degiacomi and V Erastova and MR Wilson, COMPUTER PHYSICS COMMUNICATIONS, 202, 304-309 (2016).
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. Program summary Program title: Assemble! Catalogue identifier: AEZE_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEZE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 504242 No. of bytes in distributed program, including test data, etc.: 55078538 Distribution format: tar.gz Programming language: Python 2.7.X. Computer: Workstations. Operating system: Windows, Linux, Mac OS X. RAM: Depending on molecule database size and final system size: 10-20 Mb in console mode, 30-150 Mb using the GUI Classification: 16.11. External routines: numpy, wxpython (if using the GUI) Nature of problem: Preparation of complex polymeric systems for molecular dynamics simulations with Gromacs. Solution method: Creation of polymers collections using monomer units and a Gromacs-compatible force field. Packing multiple polymer copies in a box according to desired concentration. Additional comments: User manual and tutorial with necessary input files are distributed with the program !!!!! The distribution file for this program is over 55 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: System dependent, but typically less than 5 seconds (C) 2016 Elsevier B.V. All rights reserved.
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