Dear Sir/Madam,
I want to do the RMSF analysis for my system (with ~ 1000 protein
residues). I did the simulation for 50 ns. I checked that the RMSD and
gyrate radius are converted after 30ns. So, I told the 30 to 50 ns mdcrd
files for the RMSF analysis.
I found the RMSF obtained from 30-50, 40-50 and 30-40 are different. The
max peak appears at same domain, but the relative intensity of the peaks at
different domains are different.
Would you mind to teach me whether I should still conclude the RMSF
obtained from 30-50 are reliable? Can I still claim that the simulation is
stable after 30?
Many thankssss :)
Perier
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Received on Mon May 28 2012 - 00:00:02 PDT
