Hi to all,

I am performing conventional MD (cMD) to fold my protein because it has so much coiled structures, so there is nearly no alpha helix and beta sheet secondary structures. I would like to form these secondary structures on my protein via MD simulation, but even if I have performed cMD for 1000 ns, the protein has been collapsed, yet it hasn't been folded and no secondary structure has'nt been formed. Due to these reasons, I would like to perform GaMD to accelerate and increase the efficient of my MD simulation since I am planning to perform 10-100 microsecond MD simulation, therefore it is too long and too expensive for cMD. I need to add harmonic potential to remove energetic barriers in potential graph, but I don't know how to I make it? Please could you help me if you have experience about GaMD?

Thank you for your helpness.

Sincerely.

Yunus.