There are several books:

• Essentials of computational chemistry, Cramer, ISBN 0470091827
• Essentials of computational chemistry: theories and models, Ramachandran ISBN 9783540773023
• Molecular Modelling: Principles and Applications, Leach, ISBN 978-0582382107

Which can be a good starting point to get into the field of computational chemistry. There are several more alternatives an people can probably provide more examples.

Someone already suggested the LAMMPS tutorials and this seems like an excellent choice since this was the entry-point you where asking for. 

Otherwise other free and commercial software packages like GROMACS, AMBER, NAMD and CHARMM all have similar tutorials describing the different softwares as well as implementations and allow you to follow step-by-step guides to set up and run simulations.

• http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html
• http://www.gromacs.org/Documentation/Tutorials
• http://www.charmmtutorial.org/index.php/CHARMM_Tutorial
• http://ambermd.org/tutorials/

The input usually differs, but the general procedures are mostly the same so looking at different software packages can be interesting depending on what applications you are planning for.

LAMMPS tutorials

https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_tutorials

Dear Amin,

Below is the link with the pdf slides used during a short course organized by the developers of LAMMPS.

http://lammps.sandia.gov/tutorials.html

Hope this helps

http://www.amazon.com/Understanding-Molecular-Simulation-Second-Edition/dp/0122673514

Dear Amin,

If really want to lear basics and theory behind the MD simulations, i would recommend you to code a simple MD program, just to simulate a nobel gas like argon using Lennard Jones potential, or any metallic cluster (copper crystal for example) using Morse potential. I found that "Understanding of Molecular Simulations from Algorithm to Applications" by Frenkel and Smit explains almost every basic algorithm related to MD simulations.

Also there is a classical paper http://journals.aps.org/pr/abstract/10.1103/PhysRev.136.A405

You can find a good lecture note in the 39th IFF Spring School on Soft Matter – From Synthetic to Biological Materials 2008. It's possible to order from 

Forschungszentrum Jülich

Central Library

52425 Jülich

Germany

Phone.: +49 2461 61 5368

Fax.: +49 2461 61 6103

Email: [email protected]

There are several books:

• Essentials of computational chemistry, Cramer, ISBN 0470091827
• Essentials of computational chemistry: theories and models, Ramachandran ISBN 9783540773023
• Molecular Modelling: Principles and Applications, Leach, ISBN 978-0582382107

Which can be a good starting point to get into the field of computational chemistry. There are several more alternatives an people can probably provide more examples.

Someone already suggested the LAMMPS tutorials and this seems like an excellent choice since this was the entry-point you where asking for. 

Otherwise other free and commercial software packages like GROMACS, AMBER, NAMD and CHARMM all have similar tutorials describing the different softwares as well as implementations and allow you to follow step-by-step guides to set up and run simulations.

• http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html
• http://www.gromacs.org/Documentation/Tutorials
• http://www.charmmtutorial.org/index.php/CHARMM_Tutorial
• http://ambermd.org/tutorials/

The input usually differs, but the general procedures are mostly the same so looking at different software packages can be interesting depending on what applications you are planning for.

if you want to learn basic concepts of MD simulation  start with reading simple books which explains basic concepts of MD, one of the book I referred is Molecular Dynamics Simulation: Elementary Methods by J. M. Haile. Also you can start with reading tutorials of MD program you want to use, you will also find helpful topics in discussion forums/mailing lists on the site of MD program you are interested in. Enjoy MD simulation its fun :-)