Namd is a molecular dynamics code which helps us to perform molecular dynamics simulation. For carrying out simulation for our system we need to create the system first. What are the files required to run NAMD? First we need an initial configuration file (a pdb file), next we need to specify the charges and connects in the system (given by the psf), later we specify a param file which has all the force field parameters. Finally, there is a NAMD configuration file containing information about the system parameters (example pressure) for the simulation.
In summary, the files required are:
Pdb : containing the initial configuration of the system
Psf : containing the charges and atom connections
Param : containing the forcefield parameters for our molecules
Configuration: parameters for our ms run
Script: to run the simulation in cluster/gpu/supercomputer
Here is the list of softwares required to generate the files required to use NAMD. The source of obtaining these softwares has also been mentioned. Note, this tutorial is meant for Windows OS.
GaussView : from IITG software repository : required to create the pdb
Gaussian : from IITG software repository : required to create the pdb
Packmol: from official site : helps in creating the system pdb
VegaZZ: from official site : helps in creating psf file
VMD: from official site : this will help in "visualizing" the system
NAMD: from official site: the MD source code
Notepad++: from official site : a text editor, please don't use notepad or notepad hash or whatever
Installing softwares is the most boring and tedious job of running computational simulations. Once you get a hang for it, it won't be a problem.
It's a small price you pay for getting rid of all those trifle issues of experimentation ("the reactant will arrive in 3 months", "who stole my test tube?").
At times, it might happen that a specific software doesn't work in your PC, try to figure out why it isn't working and fix it.
After you are done with installation and each of the above softwares are working fine, move to the next page.
A brief note about next page: We are trying to perform molecular simulations. But what exactly are we trying to obtain from our simulations?
This is an introductory tutorial, and here we will focus on performing a trifle density measurement of ethanol. Once you get used to the jargons and ways of the
trade, you can easily switch to finding new conformations about your beloved protein or analyzing the shape memory of your nanoparticles.