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Easy coarse-grained simulations with the SAFT-gamma Mie force field

Project description


.. figure::
:alt: raasaft-wide.jpg


Illustrative image courtesy of ` <>`__

What is raaSAFT?

- raaSAFT (pronounced "raw saft") is a Python framework for easy
coarse-grained molecular dynamics simulations.
- raaSAFT runs with HOOMD-blue as a backend, so you can use GPU power.
Initial support for using GROMACS has been added.
- raaSAFT uses the SAFT-gamma Mie force field, a coarse-graining method
which is thermodynamically consistent, and not based on tuning to
atomistic simulations
- Raasaft is a Norwegian word meaning "pure fruit syrup". Apart from
the obvious saft <-> SAFT pun, "raa" means crude/raw/\ **coarse**, so
it is twice as punny.

Installing raaSAFT


- raaSAFT uses HOOMD-blue, see the `HOOMD-blue install
guide <>`__.

- For now this is a dependency even if you want to run with GROMACS.
The non-GPU version of HOOMD-blue is sufficient.

- Note that HOOMD-blue runs on Linux or Mac OSX. Windows is not

**Simple installation:**

- System-wide install: ``sudo pip install raasaft``
- Local installation: ``pip install --user raasaft``

- To upgrade: add ``--upgrade`` after ``install``

- To start using raaSAFT: make a new folder, enter it and run the
to add the helpful directories ``tutorials/``, ``replication/`` and
- Read the "Running simulations" section below.

**Installation for advanced users / contributors:**

- Install dependencies. This includes HOOMD-blue and the Python
packages ``future`` and ``requests``.
- Clone this repo

- The ``maint`` branch should be as stable as the version on PyPi
- The ``master`` branch changes frequently and may not always be

- The ``raasaft_init`` command will not be in your path unless you put
it there.

Running simulations with raaSAFT

- Make sure you have run the ``raasaft_init`` command in the folder
where you want to run your simulations.

- Let's call this folder "trysaft".

- Look at the README.txt file in "trysaft/tutorials/" for examples of
how to use raaSAFT.
- In "trysaft/replication/" we include setups that can be used to
replicate the findings of various papers.
- In "trysaft/mysaft/" you find an example of how to add your own
models for new molecules.

- You can use these user-defined models with e.g.
``from mysaft.example import Example``
``ex = Example(count=1e3)``
- If you want to use these models in jobscripts in different
directories, add the full path to the "trysaft" folder to your
``PYTHONPATH`` shell variable, e.g.:
``export PYTHONPATH=$PYTHONPATH:"$HOME/trysaft"``
- Contributions to raaSAFT with new models are always welcome,
assuming the model has seen at least some level of validation.

Bottled SAFT

| You can get models (force field parameters) for 6000+ molecules from
our database called Bottled SAFT:
` <>`__.
| This web application provides scripts that implement the search result
in raaSAFT for you!


- The code is Free and Open Source software under the `MIT
license <>`__.


- All contributions are welcome!


- Email Åsmund at

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