Structure and energy are two sides of the same coin. When i want to examine a coin, i want to look at both sides of it.

As Eduardo said I'm agree with this. I want to add few things. Like if your protein have metal or any other things then you have to consider the same force field parameters for them also. For protein folding you'll need a long time scale simulation(micro seconds) depending upon your protein size. Or you can do enhance sampling (metadynamics) to remove the local minima. If you know the initial and final conformation of your protein then you can do targeted molecular dynamics simulation. So based on your protein you can design your work.

Regarding force field concern you can select gromos or amber or charmm. Gromacs single precision will be faster if you are planning to do long classical simulation. If you need anything let me know.

Regards

Krishna

Thank you all for your answers, I think I have to make my point more clear :)

Dear Martin Klvana, I know that the structure depends on what the calculated energy is for that state in those conditions. I also know that when they create force fields, they have to validate the data and until now I didn't find any force fields that would be validated by structure (one like that would be ideal for me, although I don't think it exists). I need a trajectory of a protein as it folds, I will be looking for knots (knot like entanglements) in it with my own code. I'm not interested in the energy or any other properties, just the structure. What I meant in my question is that I don't want to calculate binding energies or free energy, or similar things, I only need the series of structures that go from linear (-ish) to a folded state or inverse.

Dear Eduardo Basilio De Oliveira, thank you for your kind explanation of general molecular dynamics. Do you know about a paper that is using one of the CHARMm, GROMOS or AMBER force fields for protein folding or unfolding that you like, or you think is trustworthy? That would help me a lot. I have the choice of choosing my protein, it can be basically anything, since I'm only interested in the folding behavior, the process itself.

Dear Krishnendu Bera, the single precision idea is a good one, thank you for that, also the targeted molecular dynamics simulation sounds promising, since I could just use a pdb structure, generate a linear version and go from one to the other. I have the time (2-3 months) to wait for it to be finished, also the access to supercomputers with good GPU-s, and since I don't need anything special, I can choose a smaller protein. If you have any suggestions of papers that I could turn to, that you like or think it's good, that would help me a lot.

Dear all, just to make my question more clear. I only need the trajectory of the folding process. I was trying to find one online that would be freely available to use for academic purposes, but I couldn't. If you know of any that would help me even more.

I have read a comparison paper about this topic, where they compared force fields to each other based on how they perform in folding simulations, and they've came to a conclusion that one of them is way better than all the others that were tested, but I don't remember which one was the winner and I can't find the paper. The research was done by a German group and I know that they were not using GROMOS force fields because of their software choice (I think). They also rated the force fields based on a visual examination of the folding trajectory videos. If this sounds familiar to someone please look for your papers, you might have the one that I'm looking for :D

May be the following papers will help.....

Elastic models of conformational transitions in macromolecules

Moon K. Kima, Gregory S. Chirikjian, Robert L. Jernigan

Journal of Molecular Graphics and Modelling 21 (2002) 151–160

and

Exploring Protein Folding Trajectories Using Geometric Spanners

D. Russel and L. Guibas

Pacific Symposium on Biocomputing 10:40-51(2005)

Hi you can take small proteins or peptides within 150 residues. You can get many pdb structures based on size in PDB database like lysozyme. I don't know what you trying to do. But I can suggest metadynamics can help you in short time to get correct folding of protein and you can analyze the path of the folding pattern followed by your protein during md simulation by FES. You can use urea or temperature to denature your protein or unfolding your protein to simple liner peptides chain and do simulation to know the folding of the protein. You can follow my NJC 2017 paper where I unfold my protein by temperature and refolded using our synthesis ions.

Thanks

I would ask the good people at http://www.ks.uiuc.edu/Research/folding/

They have movies of folding trajectories on their site so I don't think it's too much of a leap to get a file with actual trajectories.

I've finally found my notes and the paper. Dr. Sarah Rauscher gave a talk about this at our university, MUN.

Article Structural Ensembles of Intrinsically Disordered Proteins De...

According to this study, based on some experimental comparisons, CHARMM 22 performs best. I have actually seen the trajectory videos and it very convincing, this is why I wanted this specific paper.

Check out her other works if you're interested in protein folding and MD, you'll find it useful.

https://www.utm.utoronto.ca/cps/faculty-staff/rauscher-sarah

Any other good paper is very welcome in the comments :)