[gmx-users] problem with g_rmsf

Adriana Pietropaolo adriana at ms.fci.unibo.it
Mon Feb 13 12:31:28 CET 2006

On Mon, 13 Feb 2006, Tsjerk Wassenaar wrote:

> 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

Hi, Tsjerk,
thanks for answering,
I understood that -q was the option for the comparing structure, I mean if 
I want to compare my traiectories with a solution NMR structure, I can use 
-q, because  near -q there is written "protein data bank file"...
so how can I make this compare, if I have a pdb file and my 
the option -s is associated with the xtc file, I think or not?
I wrote "zero" because If I make the least squares of the same structures 
the results must be zero....
but if -q is the option for the output,...maybe -s will be the tpr of the 
standard structure...
sorry...I'm a little bit confused...

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