[gmx-users] g_rms

andrea carotti andcar at chimfarm.unipg.it
Wed Oct 3 16:08:29 CEST 2007

Hi again,

> If you read g_rms -h like I suggested last time, you'll see that -f2 and 
> -s serve the same purpose with the former using a trajectory and the 
> latter a single structure. That document doesn't say what happens when 
> you use both... but the operation you're trying to do doesn't need both!
the -h option is my standard first step when i use all the gmx-tools and I've read and done it like every time.
I've tried to use -f2 option without using the -s and it comes out with the error "topol.tpr not found" so it's not "so optional", but it's needed also when using the -f2 option..
I've alsto tried to use the -s with my traj without using the -f2 option but it creates a matrix 2200x2200.
However the problem still remain unsolved or misunderstanded.
If i use the my only working command line
g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 

I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a mean of all the rmsd calculated for that frame in respect to the other 33 refs?

Andrea Carotti
Dipartimento di Chimica e Tecnologia del Farmaco
Via del Liceo, 1
06123 Perugia, Italy
phone: +39 075 585 5169
fax: +39 075 585 5161
www http://rpg.unipg.it
personal www http://iris.chimfarm.unipg.it/users/andcar

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