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raaSAFT

raasaft-wide.jpg

Illustrative image courtesy of www.frukt.no

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

Dependencies:

  • 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 supported.

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 command
    raasaft_init
    to add the helpful directories tutorials/, replication/ and mysaft/.

  • 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 stable
  • 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: www.bottledsaft.org.
This web application provides scripts that implement the search result in raaSAFT for you!

License

  • The code is Free and Open Source software under the MIT license.

Contribute

  • All contributions are welcome!

Contact

  • Email ├ůsmund at aaervik@gmail.com