davyyue / trajapi

API for converting bead trajectory into radial distribution function

TrajAPI

Automate the process for converting a given trajectory for a bead into the desired rdf. Establish a mapping for the coarse-grain bead and construct the corresponding coarse-grain trajectory.

... Incoming updates arriving this July 2017 to a Github repository near you ...

Getting Started

Install the following prerequisite packages, clone the repository on your local machine, and run the jupyter notebook file.

Prerequisites

Download and install the following packages:

• Python v3.6
• MDTraj v1.8.0
• MSIBI
• numpy

Installing

... Coming this July 2017 to a Github repository near you ...

Deployment

... Coming this July 2017 to a Github repository near you ...

Built With

• MDTraj - Generate and read trajectories
• MSIBI - Run pair potential optimizations using multistate-iterative Boltzmann inversion.

Authors

• Davy Yue - Vanderbilt MuMS Institute Assistant Researcher - Profile

Notable Contributors

• Timothy C. Moore - Vanderbilt MuMS Institute Graduate Researcher - Profile

• Christoph Klein - Vanderbilt MuMS Institute Graduate Researcher - Profile

  • Provided phenomenal coaching throughout API creation process
  • Supplied creative ideas in every stage of the SDLC

See also the list of contributors who participated in this project.

Citation

Details of the underlying method and its validation can be found in a published paper here.

If you use this package or MSIBI, please cite the above paper. The BibTeX reference is

@article{Moore2014,
      author = "Moore, Timothy C. and Iacovella, Christopher R. and McCabe, Clare",
      title = "Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion",
      journal = "The Journal of Chemical Physics",
      year = "2014",
      volume = "140",
      number = "22",
      doi = "http://dx.doi.org/10.1063/1.4880555"
}

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Stack Overflow for stackin' tips n' flowin' sips
• Google for bein' real legit since 1998
• Sidewalks for keeping me off the streets
• etc