AMBER: ptraj RMSD vs. RMSF

From: Steve Seibold <>
Date: Mon, 18 Sep 2006 15:54:02 -0400


I am having a major confusion on how to obtain RMSD per residue and RMSF
per residue. I have looked up on the amber web-site and it appears that
people have stated that you can get RMSDs from "autoflux" in ptraj while
others refer to it as RMSFs. Is not RMSD per residue the deviation from
crystal structure (starting structure) while RMSF per residue is the
deviation from the average (MD) structure?


The two scripts attached are what I thought was giving me the difference
between RMSD and RMSF, but when I compare the RMSD(F) output they are


Can someone help me?


Thanks Steve




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Received on Wed Sep 20 2006 - 06:07:12 PDT
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