Easy creation of polymeric systems for molecular dynamics with Assemble!

详细信息    查看全文

• 作者：Matteo T. Degiacomi^a ; ¹ ; ² ; ^{matteo.degiacomi@chem.ox.ac.uk" class="auth_mail" title="E-mail the corresponding author} ; Valentina Erastova^b ; ¹ ; ³ ; ^{valentina.erastova@durham.ac.uk" class="auth_mail" title="E-mail the corresponding author} ; Mark R. Wilson^c
• 关键词：Polymeric mixture ; Molecular dynamics ; Gromacs ; Simulation preparation
• 刊名：Computer Physics Communications
• 出版年：2016
• 出版时间：May 2016
• 年：2016
• 卷：202
• 期：Complete
• 页码：304-309
• 全文大小：2076 K

文摘

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