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 ( 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 (


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:


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


tar zxvf  NAMD*.tar.gz


To test the installation, type:



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!

Why we need a laptop to explore space chemical substance?

Daily routine

Daily routine

Computational chemistry interests several scientific communities and is expanding everyday more.

Twelve papers on the Nature
TOP 100 most cited research refers to quantum-mechanical modeling (

Two Nobel prizes in Chemistry were awarded for foundations of computational chemistry.

The 1998 Nobel prize was assigned to Walter Kohn “for his development of the density-functional theory” and to John Pople “for his development of computational methods in quantum chemistry“.

Martin Karplus, Michael Levitt, and Arieh Warshel jointly won the Nobel prize in 2013 “for the development of multiscale models for complex chemical systems”.

Molecular modeling without experiments does not exist, but in 2016 also the opposite is true; molecular modeling is more and more frequently placed side by side with experiments. Nowadays, many applied sciences are taking advantage of molecular modeling; protein catalysis, water and air pollution, pharmaceutical chemistry, and combustion science are just few of the molecular modeling application fields.

Computational chemistry provides powerfull tools to investigate those systems that can be difficult to study by experimental means only. It can support and assist the experimental scientists in the interpretation of science research where measurements are indirect or cannot be performed due to technological limitations. Here one example of the contribution of molecular modeling to applied science.

An interesting example of molecular modeling application is the detection of organic molecules in planetary atmosphere and in the interstellar medium.
New astrochemical and astrophysical models were developed to explain and support astronomical observations. Thus, spectroscopy and computational techniques were applied together to investigate the chemical and physical processes leading to the formation of organic species in planetary atmospheres and the interstellar medium.

Quantum chemistry calculations were carried out to assess the spectroscopic and thermodynamic properties of those potentially prebiotic molecules detected in space environments. (for instance:,

Lesson 0 – Download and install VMD

VMD (Visual Molecular Dynamics) is a very useful visualization software for molecular structures, available for Windows, MacOS and Linux based systems.

To download and install it follow the next steps, it’s very simple!


0 – Read the Copyright and Disclaimer: here:


1 – Choose your OS:

Go to the following page: and choose your OS package of the latest version of VMD (1.9.2 current version)


2 – Registration:

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


3- Download and proceed with the installation:

The download should start automatically.


Windows: when the download is finished the installation should start automatically.


MacOS: open the VMD disk image and drag the application in the destination folder


Linux: move the dowloaded .tar to the folder where you want to install vmd:

mv archive.tar /path-to-folder

#Untar the folder and move into it:

tar -xvf archive.tar

cd vmd***

#Create the Makefile with the command:


#Then move into the src directory and run make:

cd src/

make install

Done! Now you have VMD installed on your computer. To run it:


For Windows and MacOS users: double click on the icon

For Linux users: VMD should be alredy in your PATH; to run it just type:


in your terminal.

See also here for other images!


Andrea Di Luca

DNA pioneer Frederick Sanger dies

Frederick Sanger and a DNA model.On November 19, 2013, the English biochemist Frederick Sanger passed away. He was one among the four people to win two Nobel prizes (the others being Marie Curie, Linus Pauling and John Bardeen) and the only one to win two for chemistry; one of the most important scientists of the 20th century.
Unfortunately, his disappearance ended up in the back burner, especially on Italian media; that’s why we of think it is due to remember him in this short post. Continue reading here: Frederick Sanger

Animal testing? Aberrant!!!

Schermata 2013-09-28 alle 12.20.29

Kladderadatsch 1933 (p. 569)

“Culture Day”
Text in the cartoon: “Vivisection Forbidden”
Down: “Heil Goering (Nazi salute)”

Schermata 2013-09-28 alle 12.13.04


Kladderadatsch 1933 (p. 579)
“The Nightmare of the vivisectors”


In former times, it was possible to do without “animal testing”, but at what price?

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