Is it possible to find the regions of the protein structures most susceptible to temperature impact in terms of RMSD and RMSF , during MD simulation ?
Yes certainly, You could also consider performing simulations at multiple temperatures (maybe 3) and observe the how the flexibility of different regions/residues changes with increasing temperature. (I would argue this to be better than a single temperature simulation as it closer to what you're asking for experimentally).
Here is a good example paper for how you could approach this:
Thermostability of Enzymes from Molecular Dynamics Simulations
10.1021/acs.jctc.6b00120
(Note that order parameters as used in the above paper can also be pulled out of MD simulations quite routinely, and are provide a similar picture to RMSF).
Hope that helps
Thanks Rory for your reply ! Yes I also agree I have to perform it for multiple temperatures. But I am asking , whether there should be any parameter to decide that particular region which showing flexibility or deviations are significant or not ?
In nutshell I am describing my question : - suppose I have RMSF and RMSD graph for my protein at two different temperature , now in this can I know which region is more significant for flexibility and deviation ? OR I have to go for any statistics test ?
In the first instance you could plot on a residue by residue basis RMSF (or order parameters) to observe changes in flexibility at the residue level. Analysis of these plots should allow you to observe regions of higher/lower flexibility.
Generally, RMSD is more useful for looking at more global conformational changes. So assuming your protein is relatively stable (and not beginning to unfold or undergo fairly large scale conformational transitions) RMSF would be a better way to go I think.
Replicate runs (under the exact same conditions of course) to give you an average and standard deviation/error could be applied to see if your results are significant.
analysing sensitivity from peaks in graph is understood able and it is becoming more clear after discussion , So accordingly you by seeing graphs and comparing the reproduced graph for same parameter , we can find sensitivity . Am I right ?
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