You may use GROMACS or AMBER for MD.

Here's the link to tutorials:

http://www.mdtutorials.com/gmx/complex/index.html

http://ambermd.org/tutorials/

If you face any problem feel free to contact me.

Hope that helps!

Happy Simulating!!

Souptik Bhattacharya AMBER is commercial. You can try GROMACS

There are number of software's available to conduct the simulations studies like GROMACS, DESMOND, NAMD and may be others.

In addition, for more information, you can check out the attached link:

https://www.researchgate.net/post/which_one_is_the_best_software_for_molecular_dynamic_simulation

There is a very comprehensive tutorial on that by Justin A. Lemkul, Ph.D. one of the GROMACS developers. the tutorial can be found in the link below

http://www.mdtutorials.com/gmx/complex/index.html

Anwesh Pandey Thirumal Kumar Aliyu Adamu I tried the above suggested Gromacs and Charmm36 forcefield to conduct the simulation of my docked protein. My residue S-adenosyl methionine (SAM) in the protein is designated as UNK in the docked file. But when I tried to create topology file for the docked protein, I got a fatal error. Residue 'UNK' not found in residue topology database

Also a Warning: No residues in chain starting at UNK1 identified as Protein/RNA/DNA.

This makes it impossible to link them into a molecule, which could either be

correct or a catastrophic error. Please check your structure, and add all

necessary residue names to residuetypes.dat if this was not correct.

Problem with chain definition, or missing terminal residues.

This chain does not appear to contain a recognized chain molecule.

If this is incorrect, you can edit residuetypes.dat to modify the behavior.

look for gromacs_charmm tutorial in my RG account, there you'll find steps. However you need to bring uniformity in your labeling of ligand, perhaps it should be LIG instead of UNK. Try and then let us know.

Anwesh Pandey I changed my ligand name to SAM. Still the error is the same. Please look into it. I am not being able to create the protein topology with the command pdb2gmx

Fatal error:

Atom O in residue SAM 402 was not found in rtp entry SAM with 50 atoms

while sorting atoms.