Installation Guide


Download the code in a ZIP file or using GIT version control from the buttons at the right side. GIT way is recommended. The program is still in beta-testing and updates will be easier to install if using GIT.

Mandatory dependencies

Many of these dependencies are common packages used by python scientific community and probably you will find some of them already installed by default with some Linux distributions. Check the instructions below for further instructions on the installation process.

  • Numpy for numerical arrays handling and math operation on large data
  • Scipy for clustering, distance metrics, KDTrees and other spatial nice stuff needed for analysis
  • ScientificPython (also needed for Biskit Installation). I highly recommend to install it with NetCDF support (check at the website the compilation instructions).
  • Biskit. Nice module for dealing with PDB files and other features.
  • Matplotlib. Plotting capabilities.
  • AMBER software: Ambertools is opensource and distributed without charge. It is needed for all the process of preparation and analysis of the simulations. The MDs can be run using AMBER itself (license required) or NAMD (distributed without charge). See User Guide.

Optional dependencies

Although not mandatory, NetCDF libraries provide faster access to trajectory data and reduce disk space usage.

  • NetCDF libraries. System-wide libraries for dealing with NetCDF formatted files. Please check your system installation instructions and the easiest way to install in your machine. This should be built before installing ScientificPython module.



Dependencies installation, in principle, should be automatic. When installing pyMDMix, will try to download and install all dependencies not found (aside Ambertools which is not a python module). This will work for most of the dependencies listed above BUT for Biskit:

Biskit auto installation is not properly working and one should install it before-hand. Biskit shares most of the dependencies with pyMDMix and therefore when installing Biskit you are done also with pyMDMix. Most important dependency to Biskit is ScientificPython.

Install ScientificPython making sure it binds NetCDF libraries and is able to read NetCDF files. You can try the following command after installation to test if NetCDF was correctly bound:

Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Scientific.IO.NetCDF as ncdf

You should not get any error. E.g. like this one in my Mac OSX:

Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Scientific.IO.NetCDF as ncdf
Traceback (most recent call last):
  File "", line 1, in 
  File "/Library/Python/2.7/site-packages/Scientific/IO/", line 169, in 
    from Scientific_netcdf import *
ImportError: dlopen(/Library/Python/2.7/site-packages/Scientific/darwin/, 2): Symbol not found: _ncerr
  Referenced from: /Library/Python/2.7/site-packages/Scientific/darwin/
  Expected in: flat namespace
 in /Library/Python/2.7/site-packages/Scientific/darwin/
Locate AmberTools

Set $AMBERHOME environmental variable if you have not done it already when installing AMBER/AmberTools. This should point to the installation directory. In bash should be something like this:

daniel@pulp:~> export AMBERHOME=/path/to/amber_installation

If installing in Windows, follow these instructions to set the variable.

Install pyMDMix

After installing all the dependencies and downloading the package, unpack the zip file or get the repo version using git, move to the recently created folder and install using python.

daniel@pulp:~> unzip
daniel@pulp:~> cd pyMDMix-XXXX/
daniel@pulp_pyMDMix-XXXX/~> python install

Or using git

daniel@pulp:~> git clone git:// pymdmix
daniel@pulp:~> cd pymdmix/
daniel@pulp:mdmix/~> python install

You may require root privileges when installing the python package.
If you do not have root access, run a local installation using:

daniel@pulp:pymdmix/~> python install --user

If installation process was successful, you should be able to enter a python interactive console and load pyMDMix.

daniel@pulp:/~> python
Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyMDMix

Sometimes Biskit yields some warning messages which you should not worry if they refer to biggles or PVM. These are optional dependencies that should not affect our pyMDMix package. For example:

Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyMDMix

Warning (ignored): Could not import PVM (Parallel Virtual Machine) modules. Please check that PVM and pypvm are installed!
        Parallelisation is not available.
cudm was not imported

Warning (ignored): Could not import biggles module -- plotting is not available.
         in /home/daniel/.local/lib/python2.7/site-packages/Biskit/ line 120:
        ('No module named biggles',).