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

[mekanix]

And the other question is:
I would like to know if the result that g_rmsf -od gives is the same that I 
will get if I use the time average g_rms per residue
Thank's very much to all
mekanix writes: 

> 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
> Rodolfo  
> 
> 
> 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.  
> 
> Cheers,  
> 
> Tsjerk  
> 
> 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 dif

ferences 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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