[gmx-users] problem with g_rmsf

[X.Periole]

On Mon, 13 Feb 2006 12:50:03 +0100 (CET)
  Adriana Pietropaolo <adriana at ms.fci.unibo.it> wrote:
> I reread the manual, to be sure and -q is the option for 
>an input 
> configuration...
> 
> 

I am affraid that Tsjerk is right. -q is an option for 
output. There is a mistake in the manual ...

XAvier

>> Hi Adriana,
>> 
>> The option -q is for output and has nothing to do with 
>>the rmsf calculation.
>> In the latter case, I'm not sure what you mean with "the 
>>results is
>> different from zero". You would indeed expect the rmsf 
>>to be zero in that
>> case, except for rounding errors. So, what exactly is 
>>different from zero
>> and by which extent?
>> 
>> Tsjerk
>> 
>> On 2/13/06, Adriana Pietropaolo 
>><adriana at ms.fci.unibo.it> wrote:
>> >
>> > Hi gromacs users,
>> > I've posted last friday, but I didn't have an answer 
>>about my doubt.
>> > I've not well understand how g_rmsf makes the least 
>>squares respect to a
>> > reference structure.
>> > If I make:
>> > g_rmsf -f a.xtc -s a.tpr -q standard.pdb -od
>> > where a.tpr is the run file relative to the xtc 
>>trajectory,
>> > I don't know why if I change the standard pdb, with a 
>>run
>> > configuration, the results is the same, I thought that 
>>this part of the
>> > protein is very rigid, but if I make:
>> > g_rmsf -f a.pdb -s a.tpr -q a.pdb
>> > where the reference and input configurations are the 
>>same and a.pdb is one
>> > configuration,
>> > the results is different from zero.
>> > So I have a doubt that I' m falling in something, or I 
>>bad understand
>> > something....
>> > Somebody can help me?
>> > thanks,
>> > Adriana
>> >
>> >
>> >
>> > --
>> > _____________________________________________
>> > Adriana Pietropaolo,
>> > PhD student,
>> > dipartimento di Chimica Fisica ed Inorganica,
>> > Facolta' di Chimica Industriale
>> > Universita' di Bologna
>> > WEB:www2.fci.unibo.it/~adriana
>> > Tel 051/6446992
>> > FAX 051/2093690
>> > _____________________________________________
>> >
>> >
>> >
>> > _______________________________________________
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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
>> 
> 
> -- 
> _____________________________________________
> Adriana Pietropaolo,
> PhD student,
> dipartimento di Chimica Fisica ed Inorganica,
>Facolta' di Chimica Industriale
> Universita' di Bologna
> WEB:www2.fci.unibo.it/~adriana
> Tel 051/6446992
>FAX 051/2093690 
> _____________________________________________
> 
> 
> 
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