Re: [AMBER] RMSF in amber

From: Elvis Martis <>
Date: Sun, 6 Jan 2019 11:01:49 +0000


Load all your trajectories (.nc files) and the prmtop file in cpptraj.

Then remove the rotational and translation motions using autoimage.

Using the "atomicfluct" command you can compute the rmsf.

Using "byres" keyword to compute rmsf residuewise.

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: Akshay Prabhakant <>
Sent: 06 January 2019 14:53
To: AMBER Mailing List
Subject: [AMBER] RMSF in amber

I have multiple trajectory files for my protein system(multiple .nc files).
How to find the rmsf(root mean square FLUCTUATION) using these .nc files?
Thanks in advance.
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Received on Sun Jan 06 2019 - 03:30:02 PST
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