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

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

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.

Release History

• 1.0.7.3
  • in progress
• 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