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GROMACS modification: Yes/No
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I want to carry out an MD simulation of the proteolytic cleavage of a protein aggregate. Is it possible to do this in a computationally correct way?
Regular MD is unable to simulate the formation or breaking of covalent bonds, since it’s a classical simulation where the bonds are essentially approximated as springs, you would need to use QM/MM where you can specify the bonds you want to described with QM. QM/MM with GROMACS + CP2K
Isn’t it possible to simulate covalent bond formation with free energy/alchemical perturbation? I’m not sure whether any properties will remain quantitatively accurate upon such topological transformation
Technically it’s feasible (my understanding is that constant-pH simulations do so in order to study varying protonation states) but I’m not familiar with any in-depth study of how accurate this is for processes like proteolytic cleavage so I can’t speak to how accurate such a simulation would be