Dear Sir,
I am trying the study the correlated motion between residues for a 3ns MD simulation. I found the rmsd, ETOT, EPTOT become stable after 200ps of MD simulations. However, I found the correlation plot collected from 300-1000 ps different from that of 1000-2000ps and that collected from 2000-3000 ps.
Should we expect to see the correlation motion would be the same during the product simulation period (i.e. 200-3000ps) or would we report the last 1000 ps (i.e. 2000-3000 ps) as the representative one?
Best regards & thanks,
Cat
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Received on Mon Jul 06 2009 - 10:01:36 PDT
