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README.md

README.md

Codacy Badge Documentation Status

Pymdsetup

Introduction

Pymdsetup is a python package to setup systems to run molecular dynamics simulations. If you have already installed the package you should check our latest API documentation.

Version 1.0

This version is just an example of a functional workflow. In v0.2 Pymdsetup uses the following applications:

  1. GROMACS: Open source and widely used molecular dynamics simulation package. (http://www.gromacs.org/)
  2. SCWRL4: Application to determine the protein side chain conformations. (http://dunbrack.fccc.edu/scwrl4/)
  3. GNUPLOT: Gnuplot is a portable command-line driven graphing utility for Linux (http://www.gnuplot.info/)
  4. PyCOMPSs (optional just for parallel executions): Python library for parallel computing. (https://www.bsc.es/computer-sciences/grid-computing/comp-superscalar/programming-model/python)

Online Installation

(We are assuming that you are installing Pymdsetup in your home directory cd ~)

  1. Install CMAKE, GNUPLOT and PIP:

    sudo apt-get -y install git vim htop cmake gnuplot python-pip
  2. Install numpy biopython pyyaml requests and nose Python libraries:

    sudo pip install --upgrade pip
    sudo pip install numpy biopython pyyaml requests nose
  3. Clone the project and add the project path to the PYTHONPATH variable:

    git clone https://github.com/bioexcel/pymdsetup.git
    export PYTHONPATH=~/pymdsetup:$PYTHONPATH
    #If you want to make this change permanent in your .bashrc file:
    echo "export PYTHONPATH=~/pymdsetup:\$PYTHONPATH" >> ~/.bashrc
  4. Register in http://dunbrack.fccc.edu/scwrl4/license/index.html, download the "install_Scwrl4_Linux" executable file, run the following commands:

    chmod u+x install_Scwrl4_Linux
    ./install_Scwrl4_Linux

And follow the SCWRL4 interactive installation instructions.

  1. Download and install GROMACS 5.1:

    wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.2.tar.gz
    # From the 5.1.2 Gromacs install guide
    # http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html
    tar xfz gromacs-5.1.2.tar.gz
    cd gromacs-5.1.2
    mkdir build
    cd build
    cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
    make
    make check
    sudo make install
    source /usr/local/gromacs/bin/GMXRC
    #If you want to make this change permanent in your .bashrc file:
    echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc

No Internet connection installation using Anaconda

https://www.anaconda.com/
(Assuming that you already installed GROMACS, SCWRL4 and GNUPLOT)

  1. On your local connected computer, download Pymdsetup, Anaconda and the Biopython Anaconda package and copy them to the offline computer:

    sudo apt-get install -y git
    git clone https://github.com/bioexcel/pymdsetup.git
    wget https://repo.continuum.io/archive/Anaconda2-5.1.0-Linux-x86_64.sh
    wget https://repo.continuum.io/pkgs/free/linux-64/biopython-1.69-np113py27_0.tar.bz2
    

Copy all files to the disconnected computer

  1. On the disconnected computer:

    bash Anaconda2-5.1.0-Linux-x86_64.sh
    source .bashrc
    mv biopython-1.69-np113py27_0.tar.bz2 anaconda2/pkgs/
    conda install anaconda2/pkgs/biopython-1.69-np113py27_0.tar.bz2
    conda install --use-index-cache --offline --use-local  numpy pyyaml requests nose
    echo "~/pymdsetup" > ~/anaconda2/lib/python2.7/site-packages/pymdsetup.pth

Using Pymdsetup

Copyright & Licensing

This software has been developed in the MMB group (http://mmb.pcb.ub.es) at the BSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission (EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.