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

[Tsjerk Wassenaar]

Hi Sangeeta,

It would be helpful to us if you gave more information than "I tried
to run a simulation and it crashed". What kind of protein, any
ligands/non-standard groups. Did you perform energy minimization, etc,
etc, etc... What's in the .mdp file?

Tsjerk

On 3/15/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>
>
> 15 mar 2007 kl. 08.29 skrev sangeeta kundu:
>
> 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.
>
>
> I'm no expert, but I think a shorter timestep could be required for the
> integrator to be stable when using such high temperatures, since the atoms
> will move around quite fast.
>
>
>
>      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.
>
>
> It requires some postprocessing of the data, but the hbn- and hbm-output of
> g_hbond together contains what you need to know about the hydrogen bonds on
> an atom index basis. Now, you can easily go from the level of atoms to the
> level of residues.
>
>
>
> regards
> Sangeeta
>
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> _______________________________________________
> Erik Marklund, PhD student
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623