[gmx-users] Understanding the output of g_rmsf

Keith Ball kball at catbio.com
Wed Nov 8 02:54:32 CET 2006



I have been a bit confused by the g_rmsf output. In the manual, it says
that "g_rmsf computes the root mean square fluctuation (RMSF, i.e.
standard deviation) of atomic positions after first fitting to a
reference frame." But what *is* the reference frame?


I assume that this output is what goes to the file specified by -o
(rmsf.xvg, by default).


The -od option (which goes to rmsdev.xvg by default) is the rms
deviation "with respect to the reference structure". What reference
structure? Is that the same as the "reference frame" mentioned above? I
notice that the numbers in rmsf.svg and rmsdev.xvg are always different,
so I assume not. 


Can anyone explain the difference between what goes into the -o file,
and what goes into the -od file?


Also, if I start at a specific frame (say, -b 1000, to start 1ns into
the trajectory), is the conformation nearest t=1ns the reference


Many thanks,



Keith D. Ball, PhD
Staff Scientist
Catalyst Biosciences
290 Utah Ave
S. San Francisco, CA 94080

650-266-8661 (phone)
650-871-2475 (fax)
kball at catbio.com



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