[gmx-users] Hydrogen bond with chlorine

[Erik Marklund]

Strange. Could you send the tpr and a short xtc for me to play with?
 
Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 10 Feb 2014, at 10:11, Dhawal Shah <dhawal at squ.edu.om> wrote:

> Thanks a ton, Erik. I have looked in similar questions and found similar answers to use -contact option. But it did not help. Neither for me nor for the one who has asked the question earlier.
> 
> I am trying the following command
> 
> g_hbond -f md_2ns_nopbc.xtc -s md_2ns.tpr -num hbCl-Urea.xvg -contact
> 
> This prompts me to select the groups. I select Urea and CL as my groups. 
> 
> Eventually it still gives zero bonds/contacts.
> 
> However, rdf shows several CL around UREA.
> 
> Any ideas on this?
> 
> Thanks,
> Dhawal
> 
> 
> 
> 
> 
> 
> 
> 
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Erik Marklund [erik.marklund at chem.ox.ac.uk]
> Sent: Monday, February 10, 2014 1:55 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Hydrogen bond with chlorine
> 
> Others have asked for this functionality before and it would make sense to implement it. However, no one is working on that at the moment and I suspect no one will on the short term since the analysis framework will be overhauled eventually. For now, you can use g_hbond -contact, which allows for atoms other than [ON] to be taken into account, but will omit the angular criterion entirely.
> 
> Erik
> 
> 
> 
> Erik Marklund, PhD
> Postdoctoral Research Associate
> 
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
> 
> On 10 Feb 2014, at 09:15, Dhawal Shah <dhawal at squ.edu.om> wrote:
> 
>> HI there,
>> 
>> I have been working on simulations of Urea and Chloride based compounds. In order to analyze my results, I am trying to find hydrogen bond between urea and chlorine.
>> 
>> However, I believe, g_hbond only account for O and N atom type hydrogen bonds.
>> 
>> How can I find number of hydrogen bonds, if it includes chlorine atoms?
>> 
>> Best Regards,
>> Dhawal
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