Hello,
I would like to perform steered Molecular Dynamics (sMD) to investigate conformational changes of the protein from the initial to the final form. I've got both initial and final coordinates of the protein in a form of PDB, I'd like to conduct simulation for 100-200ns and extract intermediate structures.
Has anyone performed such study using AMBER suite and can supply any how-to?
Regards,
Rafal
I believe sMD is not a suitable method to study conformational changes since there's no evident reaction coordinate to explore. Perhaps thermodynamic integration will suit better your problem, if you're trying to calculate the Gibbs free energy. Another option would be advanced sampling methods or perturbational methods, if you want to extensively explore de conformational landscape.
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