[AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ

From: Maghsoud, Yazdan <YazdanMaghsoud.my.unt.edu>
Date: Tue, 12 Oct 2021 21:23:11 +0000

Dear Amber users, I want to make a graph including the atomic fluctuations of all atoms of a specific residue versus the frame numbers. I read the CPPTRAJ manual but couldn't figure out how to get this specific graph. The command (atomicfluct :residue-number name.dat byatom) for example gives the total atomic fluctuation of the atoms of a specific residue during the whole MD but not based on each frame:

#Atom AtomicFlx
13747.000 0.4459
13748.000 0.4473
13749.000 0.4446
13750.000 0.4476
13751.000 0.4440

As you see the above-mentioned command gives the atom numbers (13747.000) and their related fluctuation (0.4459). What I want is something like the following:

#Frame CA HA CB HB2 HB3 ....

Thanks in advance,


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Received on Tue Oct 12 2021 - 14:30:03 PDT
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