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 ?
Thanks Uttam for your reply ! And for RMSF part its clear to me now. But still I have doubt for RMSD , means how to check its sensitivity residue wise ?. In short , how to check sensitivity of all local deviation in RMSD residue wise ? .i.e.(RMSDL)
You can do Replica Exchange-MD to see the effect of temperature. Through RMSF calculate the B-Factor and check most stable part of your protein. You can also check it through PCA calculation. RMSD generally show you the deviation of whole protein or a part of protein from the initial conformation, but RMSF give you residual/atomic level information. If you want to see RMSD of a particular part of your protein, then make a group of that part of protein in your index file (gmx make_ndx) and calculate the RMSD (gmx rms) selecting that group. Hope this will help you.
- Badges
- Science topic