[gmx-users] g_hbond

[Erik Marklund]

On Mon, 2006-12-18 at 14:13 +0100, Florian Haberl wrote:
> hi,
> 
> On Monday 18 December 2006 12:34, OZGE ENGIN wrote:
> > Hi,
> >
> > I have a problem with g_hbond. I want to investigate the H bonds formed not
> > only within the protein but also between water molecules and the protein.In
> > this respect,  I select the group 0 --> 'system' option for both
> > selections, an error message like the following one appears:
> >
> > Segmentation fault
> >
> > How can I fix this problem?
> 
> Please describe your system more:
> how many atoms
> how many water molecules
> ...
> 
> Does g_hbond run with your test system (20 aa some water molecules)
> 
> I think it is a memory problem, if you take too much atoms into account 
> g_hbond can consume a little bit more memory (depends also on your options)
> 

Yes, I think so too. Could you split your analysis into different parts?
Someting like: (I) protein-protein, (II) solvent-pprotein and (III)
solvent-solvent h-bonds. That would reduce the required memory.

/Erik

> 
> >
> > Thanks in advance
> >
> > Ozge
> >
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> 
> Greetings,
> 
> Florian
> 
-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se