Follow this tutorial:

http://www.mdtutorials.com/gmx/

Hi

You can find some information in the following site:

https://web.stanford.edu/class/cs279/lectures/lecture4.pdf

Follow this tutorial:

http://www.mdtutorials.com/gmx/

I second what Anwesh mentioned. GROMACS is a quite popular molecular dynamics simulation software, and you can start it off with a regular PDB file (with some slight modifications to occupancy of each atom, if I recall correctly). They have a tutorial that walks you through the entire process, and you can adapt it relatively easily to your own protein.

This sounds like a quite complex thing to investigate using MDS - I am not extremely versed on the limitations of MDS, but if it can be done at all, it's going to require a lot of computing power. I would suggest you look around for papers that have performed MDS on such complex systems and see what parameters and algorithms they use, because choosing the wrong parameters is most likely going to result in you having to perform some lengthy and painful troubleshooting so your system doesn't blow up whenever you try to equilibrate it.

Gromacs is the best option for you. You can get a full details of how to perform MD for your specific systems here:

http://www.mdtutorials.com/gmx/

Download a pdb structure. Then choose a exact force field for your system, and follow the instructions.

Dear Benmalti, Pandey, Adams, and Mahanta, Thank you very much for your suggestions. They are so helpful for me.

Regards,

Ananda

Start by simulating something small, to see how the software works. You will also get a feel for what is possible with your available computer hardware.