hi.. I am working on the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden shoot up in the RMS at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns .i have extracted the pdbs at this particular time frames.i found that the trimer is been spilt into monomer and dimer.i wanted to know exactly what are the parameters i need to adjust during the simulation to get a stabilised modelled structure.
thanx Bhargavi
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