NAMD – lesson 0, an introduction to Molecular Dynamics

NAMD - Scalable Molecular Dynamics

NAMD – Scalable Molecular Dynamics

Molecular dynamics (from now on, MD) is nowadays an essential tool in chemical and biological research, as it has been employed in study of small organic compounds and big biomolecular machineries (http://www.nature.com/nature/journal/v497/n7451/full/nature12162.html). Its importance has been recognized in 2013 with the Nobel prize for chemistry awarded to Karplus, Levitt and Warshel for “the development of multiscale models for complex chemical systems”.

Experimental techniques such as X-ray crystallography, solution and solid-state NMR, and more recently cryo-EM help scientists to calculate the three-dimensional structures of proteins and RNA molecules, but fast-scale dynamics of these systems (i.e. conformational changes of enzymes upon substrate binding, allosteric regulation) are unaccessible with these approaches. MD simulations allow the investigator to observe the system of interest with atomic resolution and to evaluate the overall and local motion of the system subunits. To give an example of how MD is not just a theoretical tool but could impact everyday life, new generation drugs for HIV and HCV have been designed using the dynamic substrate envelope model (http://www.ncbi.nlm.nih.gov/pubmed/21762811).

 

NAMD is a software developed by Klaus Schulten’s group at University of Illinois in 2005 to carry out MD simulations using a broad set of force fields. Although NAMD and other MD softwares are often run on computer cluster due to the impressive computational power required, a local installation is useful to test the configuration scripts before submission of the actual job.

 

Here we show how to download and set up the current version of NAMD (2.11) for a local installation.

 

0 – Read the Copyright and Disclaimer:

http://www.ks.uiuc.edu/Research/namd/license.html

 

1 – Download the archive for your system (Windows, MacOS or Linux).

Since we will run NAMD on a local computer, we don’t care about particular builds, so just download the basic version (Win64, MacOSX-x86_64 or Linux-x86_64).

 

2- Registration:

Register to the following page (choose a username and password) , then log in and accept the Terms of the License

 

3 – Extract the archive to your favorite destination.

 

For Linux and MacOS:

 

go to your home directory:

cd ~

 

create a directory for NAMD:

mkdir NAMD

 

move the archive to the created directory:

mv NAMD*.tar.gz NAMD

 

extract the archive

cd NAMD

tar zxvf  NAMD*.tar.gz

 

To test the installation, type:

./namd2

 

You will see the software fail because we don’t have yet a configuration file, but it will display some information regarding your system.
Stay tuned for the next lessons!