Dear Abhinav, This is a bit tricky. We implemented the geminate recombination model some time ago, but have taken it our of the gmx hbond tool because it complicates the code quite a lot.
That said, if you want to use that old code you first need to "pbc-unwrap” your trajectory using trjconv -nojump. Try that and see if you get more reasonable output. Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 13 Sep 2017, at 06:16, Abhinav Srivastava (P14CHM002) <srivastav...@iitj.ac.in<mailto:srivastav...@iitj.ac.in>> wrote: Dear Gromacs Users, Kindly consider this as my query mail as in the last mail, subject line was not complete. I apologize for the same . I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk water (TIP4P/2005 water) using reversible geminate recombination as mentioned in Markovitch et al., J. Chem. Phys.,129,084505(2008). Following is the command which I have used : g_hbond -f NVT.xtc -s NVT.tpr -n bulk-water.ndx -b 0 -e 100 -P 1 -temp 308 -geminate dd -ac Cdd-bulk-water.xvg I have simulated two systems viz. smaller system consisting of 851 water molecules and a bigger system consisting of 1944 water molecules. I am not able to get t^-3/2 scaling in hydrogen bond correlation function for Cdd case in both these systems. It would be nice if you can please help me. Thanks in advance. -- *Abhinav Srivastava* *Research Scholar* Indian Institute of Technology, Jodhpur Rajasthan -- 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<mailto: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.