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[Licence| Download | New Version Template] afbe_v1_0.tar.gz(29732 Kbytes)
Manuscript Title: raaSAFT: a framework enabling coarse-grained molecular dynamics simulations based on the SAFT-γ Mie force field
Authors: Åsmund Ervik, Guadalupe Jiménez Serratos, Erich A. Müller
Program title: raaSAFT
Catalogue identifier: AFBE_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 212(2016)161
Programming language: Python.
Computer: Any computer, optionally with Nvidia GPU(s).
Operating system: Linux, Mac OSX.
RAM: Depends on number of atoms and cutoff size
Keywords: Molecular Dynamics, GPU, HOOMD-blue, GROMACS, coarse-grained, SAFT-γ Mie.
Classification: 7.7, 16.13.

External routines: HOOMD-blue [1][2]

Nature of problem:
The behaviour and properties of simple and complex fluids, including mixtures

Solution method:
Coarse-grained molecular dynamics using the SAFT-γ Mie force field [3].

Ions and ionic compounds are not supported yet. Jobscripts running with Python 2 require HOOMD-blue v1.3 or newer; for Python 3 there is no such restriction.

Unusual features:
Uses object-oriented programming to make reuse and sharing of models very simple. Allows the simulation to be set up and executed completely programatically, i.e. without the use of a GUI or preprocessor. Force field parameters are available from an online database with more than 6000 molecules, http://www.bottledsaft.org [4].

Additional comments:
The code is hosted on http://bitbucket.org/asmunder/raasaft

Running time:
On a single high-end GPU in 2015 (Nvidia K40), around 2.5 nanoseconds per hour of walltime for a million atoms (not counting hydrogens).

[1] J. A. Anderson, C. D. Lorenz, A. Travesset, General purpose molecular dynamics simulations fully implemented on graphics processing units, Journal of Computational Physics 227 (2008) 5342-5359.
[2] J. Glaser, T. D. Nguyen, J. A. Anderson, P. Lui, F. Spiga, J. A. Millan, D. C. Morse, S. C. Glotzer, Strong scaling of general-purpose molecular dynamics simulations on GPUs, Computer Physics Communications 192 (2015) 97-107.
[3] E. A. Müller, G. Jackson, Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations, Annual review of chemical and biomolecular engineering 5 (2014) 405-427.
[4] Å. Ervik, A. Mejía, E. A. Müller, Bottled SAFT: a web app providing SAFT-γ Mie force field parameters for thousands of molecular fluids, In preparation. (2016).