Fill the README

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README.md

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 # Martinize2 and vermouth: The ultimate resolution transformation tools
 
-TODO: documentation
+Martinize2 is a rewrite of [Martinize]. It is aimed at producing
+coarse-grained structures and topologies from an atomistic structure. Martinize
+is primarily developed for the [Martini] coarse-grained force field and the
+[Gromacs] simulation engine. However the architecture of the program will
+allow us to support a broader range of force fields and simulation engines in
+the future.
+
+Vermouth (for VERsatile, MOdular, and Universal Tranformation Helper) is the
+python library that powers Martinize2. It allows to describe and apply
+transformation on molecular structures and topologies using graph algorithms.
+
+## Disclaimer
+
+**Both Martinize2 and vermouth are at a prototype stage. DO NOT USE IN
+PRODUCTION.**
+
+## Installation
+
+Martinize2 and vermouth require python 3.4 or greater. They can be installed
+using the `pip` command:
+
+ pip install git+https://github.com/jbarnoud/martinize2.git#vermouth
+
+The behavior of the `pip` command can vary depending of the specificity of your
+python installation. See the [documentation on installing a python
+package][pipdoc] to learn more.
+
+## Basic usage
+
+Installing Martinize2 and vermouth with `pip` adds the `martinize2` program to
+the research PATH. You can see the available option of the program by running:
+
+ martinize2 -h
+
+At the moment, martinize2 tries to reproduce the interface of the original
+Martinize. You can find explanations on how to use Martinize on the [Martini
+tutorials]; in most cases, replacing calls to `martinize.py` by calls to
+`martinize2` should produce similar results.
+
+The documentation of the vermouth python library will come soon.
+
+## License
+
+Martinize2 and vermouth are distributed under the Apache 2.0 license.
+
+ Copyright 2018 University of Groningen
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http:https://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+The [full text of the license][license] is available in the source repository.
+
+## Contributions
+
+The development of Martinize2 and vermouth is done on [github]. Contributions
+are welcome as [bug reports] and [pull requests]. Note however that the
+decision of whether or not contributions can give authorship on the resulting
+academic paper is left to our sole discretion.
+
+[Martinize]: https://github.com/Tsjerk/Martinize
+[Martini]: http:https://cgmartini.nl
+[Martini tutorials]: http:https://cgmartini.nl/index.php/tutorials-general-introduction-gmx5
+[Gromacs]: http:https://www.gromacs.org
+[pipdoc]: https://packaging.python.org/tutorials/installing-packages/#installing-packages
+[license]: https://github.com/jbarnoud/martinize2/blob/master/LICENSE
+[github]: https://github.com/jbarnoud/martinize2
+[bug reports]: https://github.com/jbarnoud/martinize2/issues
+[pull requests]: https://github.com/jbarnoud/martinize2/pulls