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I have generated an RMSD curve for monomeric insulin at three different pH values and obtained the following graph.
What sort of information can I elucidate from this graph?
There are consistent fluctuations at all three different pH values for insulin across the time series and I assume that this suggests that the structure undergoes changes in terms of it structure. Insulin at pH 2 seems to undergo maximum structural deviation of the three. They all relax towards the end of the time series, which is a generally expected trend.
Is my RMSD value too high? What does this suggest? I have read papers that have RMSD values below 3 Angstroms for proteins.