htpolynet

High-Throughput Polymer Network Atomistic Simulations

htpolynet is a Python utility for generating atomistic models of cross-linked polymer networks together with appropriate topology and parameter files required for molecular dynamics simulations using Gromacs. It is intended as a fully automated system builder requiring as inputs only the molecular structures of any monomer species, a description of the polymerization chemistry, and a handful of options describing desired system size and composition. htpolynet uses the Generalized Amber Force Field for atom-typing and parameter generation.

Installation

From PyPI:

pip install htpolynet

From conda-forge:

conda install -c conda-forge htpolynet

From source:

git clone git@github.com:AbramsGroup/HTPolyNet.git
cd HTPolyNet
pip install -e .

Once installed, the user has access to the main htpolynet command.

IMPORTANT NOTES: The programs antechamber, parmchk2 and tleap from AmberTools must be in your path. These can be installed using the ambertools package from conda-forge or compiled from source. You also need Gromacs installed so gmx is in your path. The examples show how to build input monomer structures using OpenBabel, so to use them you need obabel in your path as well.

Documentation

Please consult documentation at abramsgroup.github.io/htpolynet.

Release History

• 1.0.9
  • minimum_bondcycle_length parameter added to allow for cyclic polymerization above a certain threshold length
  • bugfixes:
    • rings not transferred from monomer templates if they are pre-parameterized
    • atom indexes in bondchain structure not remapped after atom deletion
• 1.0.8
  • uses chordless_cycles to find rings; ringidx no long unique atom attribute; improved ring-pierce detection
• 1.0.7.2
  • moved Library package to resources subpackage of HTPolyNet.HTPolyNet
• 1.0.6
  • gmx-style analyze subcommand added
• 1.0.5
  • Post-build MD simulations and plotting functionalities added
• 1.0.2
  • Enhanced molecule-network graph drawing in the plot subcommand
• 1.0.1
  • Fixed atom index assignment issue for systems with more than 100,000 atoms
• 1.0.0
  • First release
• 0.0.1
  • Initial beta version

Meta

Cameron F. Abrams – cfa22@drexel.edu

Distributed under the MIT license. See LICENSE for more information.

https://github.com/cameronabrams

https://github.com/AbramsGroup

Contributing

1. Fork it (https://github.com/AbramsGroup/HTPolyNet/fork)
2. Create your feature branch (git checkout -b feature/fooBar)
3. Commit your changes (git commit -am 'Add some fooBar')
4. Push to the branch (git push origin feature/fooBar)
5. Create a new Pull Request