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 source:

git clone [email protected]:AbramsGroup/HTPolyNet.git
cd HTPolyNet
pip install -e .

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

IMPORTANT NOTE: 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.

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 – [email protected]

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