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Coarse-grained simulations with the SAFT-gamma Mie force field

Project description

  • raaSAFT (pronounced “raw saft”) is a Python framework that makes it easy to set up 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 powerful coarse-graining method that gives accuracy comparable to atomistic models, with runtimes that are orders of magnitude shorter.
  • 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.

Installation

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:

pip install raasaft

# or to upgrade
pip install --upgrade raasaft

# To start using raaSAFT:
mkdir raasaft && cd raasaft
raasaft_init
# You now have the helpful directories tutorials/ replication/ and mysaft/
ls

# 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 the repo at http://bitbucket.org/asmunder/raasaft
    • The maint branch should be as stable as the version on PyPi
    • The master branch changes frequently and may not always be stable
  • You probably want to add the repo directory to your PYTHONPATH.

Running simulations with raaSAFT

  • Look at the README.txt file in raasaft/tutorials/ for examples of how to use raaSAFT.
  • In raasaft/replication/ we include setups that can be used to replicate the findings of various papers.
  • In raasaft/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 raasaft folder to your PYTHONPATH shell variable (put this in your .bashrc file to make it permanent), e.g.:
    export PYTHONPATH=$PYTHONPATH:”/path/to/raasaft”
  • 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:

http://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 Aasmund at aaervik@gmail.com

Project details


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