bakery

Generic adaptive resolution approach to reverse mapping of polymers

Structure:

• doc/ - the sphinx documentation

• src/ - the main code

  • start_backmapping.py - run the MD simulation with backmapping
  • prepare_files.py - prepare hybrid files

• examples/ - the set of examples

Requirements:

• networkx >= 2.0
• modified espressopp - https://github.com/bakery-cg2at/espressopp
• numpy

If you like to use the method in your work, please cite following materials:

@article{doi:10.1021/acs.jctc.6b00595,
  author = {Krajniak, Jakub and Pandiyan, Sudharsan and Nies, Eric and Samaey, Giovanni}
  title = {Generic Adaptive Resolution Method for Reverse Mapping of Polymers from Coarse-Grained to Atomistic Descriptions},
  journal = {Journal of Chemical Theory and Computation},
  doi = {10.1021/acs.jctc.6b00595},
  note ={PMID: 27685340},
  URL = { http://dx.doi.org/10.1021/acs.jctc.6b00595},
}

If in your work you willing to reverse map complex polymer structures like polymer networks, please cite following article:

@article {JCC:JCC25129,
    author = {Krajniak, Jakub and Zhang, Zidan and Pandiyan, Sudharsan and Nies, Eric and Samaey, Giovanni},
    title = {Reverse mapping method for complex polymer systems},
    journal = {Journal of Computational Chemistry},
    issn = {1096-987X},
    url = {http://dx.doi.org/10.1002/jcc.25129},
    doi = {10.1002/jcc.25129},
    pages = {n/a--n/a},
    keywords = {molecular dynamics, simulation, soft matter, polymer networks, reverse mapping, epoxy, melamine, dendritic, polyester},
}

and the software package:

@misc{jakub_krajniak_2017_819783,
  author       = {Jakub Krajniak},
  title        = {{bakery-cg2at/bakery: bakery: reverse mapping tool 
                   v2.0}},
  month        = jun,
  year         = 2017,
  doi          = {10.5281/zenodo.819783},
  url          = {https://doi.org/10.5281/zenodo.819783}
}

Please note that if you use in your published work any modified version of this software package then you are obliged to publish your modified code.