Lammps, VMD, MDAnalysis, Software, Python

Molecular Dynamics lunch box. How to install software on your machine?

Posted by Vasilii Triandafilidi on April 8, 2015

What do we need?

In order to do Molecular Dynamics one needs to install essential software.

We’ll need to install several packages in order to be fully ready for our simulations:

  1. Molecular Dynamics package [lammps]_
  2. Python installation with all essential packages [anaconda]_
  3. Molecular Trajectory Analysis package [mdanalysis]_ , [pizza]_ , [moltemplate]_
  4. Tool to visualize your trajectory [vmd]_

How to install Lammps?

To install Lammps one may follow one of these tutorials

The easiest way to install [lammps]_ on Ubuntu machines would be :

sudo add-apt-repository ppa:gladky-anton/lammps
sudo apt-get update
sudo apt-get install lammps-daily

#it builds with FFTW3 and OpenMPI.

lammps-daily -in in.lj

#To get a copy of the current documentation and examples:
#which will download the doc files in /usr/share/doc/lammps-daily-doc/doc and example problems in /usr/share/doc/lammps-doc/examples.
sudo apt-get install lammps-daily-doc

On my mac it was very straight-forward as well:

brew tap homebrew/science
brew install lammps
#brew install lammps --HEAD --with-mpi

On Windows one may download a setup file and install it, or install it using lammps_cygwin

How to install Anaconda Python distribution?

I love Python, i think it is arguably the easiest “heavyweight” programming language to learn, it has enormous potential for your tasks, and a wonderful community. For scientific use one may download an open-source distribution called Anaconda which has everything a scientist may need. On any *nix machine one may install it by downloading .sh file, and running bash Anaconda*.sh

Installing any other Python packages will be as easy as: pip install <name of the package>

So to install Molecular Dynamics trajectory Analysis program one can install [mdanalysis]_, which is a Python based program, with an easy interface and good community.

To install it one simply needs to:

pip install MDAnalysis

To install [pizza]_ and [moltemplate]_ one simply needs to download the .tar files, extract them and add to the path To do that we need to add this lines to ~/.bashrc file

export PATH="$PATH:/path_to_moltempalate/moltemplate/src"
export MOLTEMPLATE_PATH="/path_to_moltempalate/moltemplate/common"
export PYTHONPATH="$PYTHONPATH:/path_to_pizza/pizza-2Jul14/src"

Visualizing Molecular Dynamics Trajectory

To visualize MD trajectories, we need to install [vmd]_. To do that on Linux systems, we need to go to their website and download a .tar file.

tar -xzvf vmd.tar.gz
cd vmd/

After downloading and untaring the archive it is all gravy: We just need vim configure, and change home_bin_dir=..,`home_library_dir` to where we want VMD to be.

On mac systems just needs to download a .dmg file and install it by just clicking it. Sometimes we also need to specify the location of the executable:

# vmdappdir='/Applications/'
    # (change it to where vmd lies, obviously ;))
alias vmd='"$vmdappdir/Resources/" $\*'
alias textvmd="vmd -dispdev text $\*"