[gmx-users] g_hbond problems

andrea.correa at unina.it andrea.correa at unina.it
Fri Mar 10 10:52:03 CET 2017

I am trying to analyze the hydrogen bonds of my simulations by g_hbond.
I am using an index file where  I created two groups: one with  
acceptor atoms (carboxylic oxygen atoms in my structure) and another  
group with the water molecules.

I got a segmentation fault with the message:

> Select a group: 6
> Selected 6: 'PEI_&_OC'
> Select a group: 3
> Selected 3: 'Water'
> Checking for overlap in atoms between PEI_&_OC and Water
> Calculating hydrogen bonds between PEI_&_OC (1296 atoms) and Water  
> (258 atoms)
> Found 86 donors and 1382 acceptors
> Reading frame       0 time 10000.000   Will do grid-seach on  
> 15x15x15 grid, rcut=0.35
> Segmentation fault (core dumped)

The number of donors is correct (I have 86 water molecules) but the  
number of acceptors is not.

Please, can someone tell me what I am doing wrong?

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