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profasi

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  • Sandipan Mohanty's avatar
    Sandipan Mohanty authored
    prf_test.sh is used to run some executables like mimiqa and compare
    the result with known correct answers. The small adjustment we
    do here is to restrict the comparison to the last line of output
    from the program run. This way, we are free to have other output
    from those programs as long as the numeric answer is printed last.
    24a62f03
    History

    ProFASi: Protein Folding and Aggregation Simulator

    Email: profasi@thep.lu.se
    Home Page: http://cbbp.thep.lu.se/activities/profasi/
    Version control (git): https://gitlab.version.fz-juelich.de/slbio/profasi

    Disclaimer: This version of ProFASi is being developed for release during the CECAM workshop "Atomistic Monte Carlo Simulations of Bio-molecular Systems" (https://www.cecam.org/workshop-details/atomistic-monte-carlo-simulations-of-bio-molecular-systems-1401 ) to be held in September 2025. This is work in progress, and should not be used for production simulations. This branch contains some experimental code and requires very up to date tools (CMake >= 3.30, Ninja >= 1.10). At present, because of our use of C++23 standard library modules ("import std;"), only Clang 18.1 or newer can be used to compile this branch. Although support for the standard library module in GCC is improving, the combination CMake+GCC has not yet been successfully tested with ProFASi.

    For normal use, please checkout and use the branch V200 instead.

    PROFASI (PROtein Folding and Aggregation SImulator) is a C++ program package for Monte Carlo simulations of protein folding and aggregation. It provides an implementation of an all-atom protein model with fixed bond lengths and bond angles, an implicit water simplified force field, and a set of tools to perform Monte Carlo simulations with the model. PROFASI version 2.1 introduced a plugins based extensible framework for Markov Chain Monte Carlo simulations involving proteins.

    Development

    ProFASi is mainly developed at

    • Simulation Laboratory Biology, Jülich Supercomputing Centre, Forschungszentrum Jülich, Germany
    • Division of Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University Sweden.

    Installation

    For software requirements and installation procedure take a look at the installation instructions.

    Note

    Operating systems

    ProFASi development takes place almost entirely on Linux, and this program is most often deployed on HPC systems, where Linux is practically the only relevant OS. But we have found that the ProFASi source code compiles using the same procedure described above on Mac OSX. ProFASi needs significant changes to compile under Microsoft Windows, but it has not been a priority. It is our aim to eventually also support Windows, at least for the parts of ProFASi meant to run on a laptop.