[gmx-users] help me with g_rmsf...

mekanix mekanix at aruba.it
Wed Oct 5 14:23:47 CEST 2005

Hi Tsjerk, thank you for the answer!
But my problem is... I can't completely understand
this difference... Maybe rms deviation is a sort of mean value
and rmsf a sort of standard deviation?
Can you explain me in few words the difference?
Thank's very much

Hi Rodolfo, 

Reading the help (g_rmsf -h) tells that "with the option -od the root mean
square deviation with respect to the reference structure is calculated",
which is quite different from the root mean square fluctuation of an atom
around its average position, which is what you get with -o. 



On 10/5/05, mekanix <mekanix at aruba.it> wrote:
> Hi to all gmx users,
> I'm a new gromax user and I use it for my thesis.
> I have a question for you about the g_rmsf tool...
> I can't understand which is the difference between
> using the -o and -od options for the outputs file...
> I mean... which kind od results are given by the 2 options
> and which are the differences between them? 
> Another question is: one of those two results is maybe
> the time average of g_rms per residue? 
> Thank's to all
> Rodolfo.
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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