Hello everyone.

I have been trying to “visualize” in silico the denaturation process of a protein with 295 residues. However, despite testing dynamics with 100 and 200 ns, and temperatures such as 400, 500, 700 and even 800K, the RMSD, RG and SASA graphs do not “demonstrate” unequivocally the destruction of the tertiary structure. Attached are comparative images of the mesophilic protein PDB 6eqe compared to PDB 6aid, a protein thermophilic from the same family. I expected significant differences over time, but I do not see this in the graphs. I would like to discuss the results and ways to “visualize” protein denaturation in silico.

Thank you all.