RMSD values

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Hi guys,

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.

Honestly, nothing. A single trajectory of 10 ns under each condition is insufficient to conclude anything, and you’ve only got one data point per nanosecond.

Every protein is different. Some are rock solid and others are highly dynamic. Are you simulating a monomer of insulin? Hexamer? RMSD is an extrinsic property.

What do your eyes tell you about how much the structures are changing? Loops are flexible and systematically elevate RMSD in ways that tell you nothing about actual stability.