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README.md

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[![Build Status](https://travis-ci.org/jag1g13/pycgtool.svg?branch=master)](https://travis-ci.org/jag1g13/pycgtool) [![Documentation Status](https://readthedocs.org/projects/pycgtool/badge/?version=master)](http://pycgtool.readthedocs.io/en/master/?badge=master) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.259330.svg)](https://doi.org/10.5281/zenodo.259330)
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# PyCGTOOL
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Please see http://pycgtool.readthedocs.io/en/master/ for full documentation.
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Please see http://pycgtool.readthedocs.io/en/master/ for full documentation.
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A Python program for automated generation of coarse-grained molecular dynamics models from atomistic simulation trajectories.
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If you experience problems or wish to see a new feature added please [file an issue](https://github.com/jag1g13/pycgtool/issues).
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If you find this useful, please cite as : `Graham, J. (2017). PyCGTOOL, https://doi.org/10.5281/zenodo.259330`
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If you find PyCGTOOL useful, please cite our JCIM paper https://doi.org/10.1021/acs.jcim.7b00096.
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```bibtex
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@article{Graham2017,
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author = {James A. Graham and Jonathan W. Essex and Syma Khalid},
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doi = {10.1021/acs.jcim.7b00096},
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issn = {1549-9596},
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issue = {4},
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journal = {Journal of Chemical Information and Modeling},
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month = {4},
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pages = {650-656},
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title = {PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories},
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volume = {57},
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url = {https://pubs.acs.org/doi/10.1021/acs.jcim.7b00096},
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year = {2017},
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}
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```
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## Usage
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Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND. These files provide the atomistic-to-CG mapping and bonded topology respectively. Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory. The format of these files is described in the [full documentation](http://pycgtool.readthedocs.io/en/master/).

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