diff --git a/README.md b/README.md index ff69d2f..a948b60 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,8 @@ [![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) - # PyCGTOOL -Please see http://pycgtool.readthedocs.io/en/master/ for full documentation. +Please see http://pycgtool.readthedocs.io/en/master/ for full documentation. A Python program for automated generation of coarse-grained molecular dynamics models from atomistic simulation trajectories. @@ -22,7 +21,23 @@ This version has several advantages over the original C++ implementation CGTOOL: If you experience problems or wish to see a new feature added please [file an issue](https://github.com/jag1g13/pycgtool/issues). -If you find this useful, please cite as : `Graham, J. (2017). PyCGTOOL, https://doi.org/10.5281/zenodo.259330` +If you find PyCGTOOL useful, please cite our JCIM paper https://doi.org/10.1021/acs.jcim.7b00096. + +```bibtex +@article{Graham2017, + author = {James A. Graham and Jonathan W. Essex and Syma Khalid}, + doi = {10.1021/acs.jcim.7b00096}, + issn = {1549-9596}, + issue = {4}, + journal = {Journal of Chemical Information and Modeling}, + month = {4}, + pages = {650-656}, + title = {PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories}, + volume = {57}, + url = {https://pubs.acs.org/doi/10.1021/acs.jcim.7b00096}, + year = {2017}, +} +``` ## Usage 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/).