From: Elvis Martis <>
Date: Mon, 3 Dec 2018 04:51:24 +0000

I guess you may want to look at root mean square fluctuations (rmsf) of the backbone atoms using different solvents, you should be using the "atomicfluct" command with atom masks that define backbone atoms as ".C,CA,O,H,N" and using a flag "byres" which gives the atomicfluct by the residue number.
The rmsd will tell you how the system has moved with time with respect to the reference frame.
the commands should be as follows"
loadparm xyz.prmtop
reference xyz.inpcrd
rms backbone :1.CA,C,N,O,H out bb.agr ref
atomicfluct out rmsf.agr :1.CA,C,N,O,H byres

Hope this helps

Best Regards
Elvis A F Martis
Molecular Simulations Group,
Department of Pharmaceutical Chemistry,
Bombay College of Pharmacy,
Kalina, Santacruz [E],
Mumbai 400098,
Institute Web-address:
Research Group Web-address:
Personal Web-address:

From: Xiaoyu Wang <>
Sent: 03 December 2018 05:58
Subject: [AMBER] RMSD vs RMSF

Dear all,

Basically, I want to measure the backbone atoms position differ respect to some reference state, for example, the first frame. By this way, I can know how much those backbone atoms fluctuated in different solvents after translation and rotation to the best comparison position. I have only one structure in the solvent. When I read the manual, there are many cpptaj commands like atomicfluct, rmsd, rms2d, drms... I am confused about using those commands. If I understand the manual rightly, am I right to use rmsd then atomicfluct to achieve my goal?
For example,
rmsd backbone :1.“backbone sites” out bb.agr ref xxx.inpcrd
atomicfluct out rmsf.agr :1.“backbone sites” bymask

I will appreciate any help.

Best wishes,
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Received on Sun Dec 02 2018 - 21:00:03 PST
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