Dear Users, I've created two different models of the same transmembrane protein. These two models were created using homology approach using two different templates (both with similar sequence similarity to the sequence of the target protein). Next, I did two separate 25ns simulations of those two obtained protein models in water and lipid environment. RMSD value calculated using g_rms reaches about 3.5 A after 10 ns in two simulations and stays stable for the rest of the MD time.
What I want to do is to obtain a plot of RMSD between those two models (model one vs model two) for each corresponding frame of those two MD simulations (I just want to add that the length of protein chain is different in both protein models). Is there a script available from gromacs tools which could be used for this? Could you give me some sugestions how to treat this problem? Thank you in advance. Michal
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