bioexcel/pymdsetup

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.

5. 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

2. 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).

• (c) 2015-2017 Barcelona Supercomputing Center
• (c) 2015-2017 Institute for Research in Biomedicine

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