[gmx-users] problem regarding "mdrun" and "g_hbond"

Mark Abraham mark.abraham at anu.edu.au
Thu Mar 15 13:45:45 CET 2007

> Dear all,
>         I gave a simulation run of a protein using G43a1force field at
> 523K using Berendson's  Temperature  coupling for 10 ns, But three
> times it failed with the messege "segmentation fault" , without
> giving any other error messege. Previously I ran the simualtion of
> the same protein at lower temperature, (upto 473K) , and in all
> cases it ran successfully, but when I used the temperature of 523
> K it failed, I can not debug, please help.

What was your minimization and equilibration protocol? If that was
reasonable, then try a smaller integration timestep.

>        I have another question, Is there any way of analysing hydrogen
> bonds on a residue basis? I mean to say how can  I get the
> distribution of HBond over residue number, I  looked at g_hbond ,
> but I could not get it.

No idea.

Please seperate different topics into different posts. That way people
with expertise in one problem and not the other can use their time more
efficiently. Yes, it's more work for you, but who is asking for the free
help here? :-)


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