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-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Erik Marklund [erik.markl...@chem.ox.ac.uk] Sent: Monday, February 10, 2014 1:55 PM To: gmx-us...@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 <dha...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
