Hello All, I have done simulation for 1ns on a protein dimer using GROMOS96 43a1 force field. I want to study if the protein is stable as a dimer or not, so can you please give me some suggestion as to what analysis I could do for the same. I checked g_rms after the simulation, graph which I am getting is like, first rmsd is increases rapidly to 0.2nm for for 0.1 ns and then till 0.8 ns it still increased to 0.3 nm and still there are more fluctuations but and it decreses again to 0.28 nm at 0.1 ns.
So what could i infer about the stability of the protein as a dimer from this data. Thanks in advance. Regards -- Sonali Dhindwal
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