From: Xiaoyu Wang <xwang181.hawk.iit.edu>
Date: Sun, 2 Dec 2018 18:28:45 -0600

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 - 16:30:01 PST
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