I performed 1 us MD simulation of a protein-protein complex. After about 200ns the complex seemed to start to disassociate and continued partially dissociated 70% of the simulation after that it returns to its initial position (bound).
This system has a mutation that drastically decreases the binding affinity and the simulation results seemed to agree with experimental data. But I am wondering if this partial dissociation is a random thing or could be due to the effect of the mutation.
Can anyone help me with that?
Best,
Nubia P. Toman
PhD student, Bioinformatics
Universidade Federal de Minas Gerais