[gmx-users] Re: g_hbond error "Your computational box has shrunk too much"

Marie-Pierre Durrieu Marie-Pierre.Durrieu at ibpc.fr
Wed Oct 18 15:17:00 CEST 2006

andrea carotti wrote:

>>Is it correct? Did you plot the box volume as a function of time?
>>You can use g_hbond for different stretches of the trajectory and 
>>combine the results manually.
>Thanks for the fast reply.
>I'm only trying to monitor the hbond formation with the " basic" command
>g_hbond -f m93_newtraj.trr -s topol.tpr -n
>and giving to the groups selection two different parts of my protein (i've made an index file)..and then the programs suddenly stop.
>the default output (-num) should be the total number of hbond per frame.
>Please help me again

I had the same message error when I was using g_hbond with a trajectory 
from an implicit solvent simulation, but with a tpr that I had built 
from an explicit solvent simulation (yes, I know, that's not very 
clever). The xtc file and the tpr file contained only my protein, that's 
why I didn't have any problem with some tools like g_saltbr, g_rms... 
but g_hbond was upset with the two different box informations.

I don't know if it can help you. But try to see if it is the same box in 
your trajectory and the tpr file.


Marie-Pierre Durrieu
Institut de Biologie Physico-Chimique
13 rue Pierre et Marie Curie
75 005 Paris - FRANCE
e-mail : marie-pierre.durrieu at ibpc.fr
Tel: +33 15841 5161

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