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Hi, 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
frame/structure? Many thanks, Keith ============================ http://www.catbio.com |
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