AMBER Archive (2009)

Subject: [AMBER] ptraj correlation

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Jun 18 2009 - 08:47:01 CDT

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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