[gmx-users] g_hbond

[OZGE ENGIN]

Hi, 

I use the 3.3.1 version of gromacs.

My system consists of a capped alanine residue embedded in a box of 500 water molecules. When I select the group 1 option ( only capped alanine residue) there is no error; however, an error occurs due to selection of the whole system (group 0 option). I want to investigate the hydrogen bonds not only formed within the protein but also between the protein molecule (capped alanine residue) and water molecules. 

Moreover, i could not understand the memory problem. Could you explain it in detail,please?

Thanks in advance 

Ozge

-----Original Message-----
From: Erik Marklund <erikm at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Mon, 18 Dec 2006 13:48:18 +0100
Subject: Re: [gmx-users] g_hbond

On Mon, 2006-12-18 at 13:34 +0200, 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?

That's hard to say. Which version are you running?

>  
> Thanks in advance
>  
> Ozge
> 
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/Erik

-- 
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

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