Hi Mark,
I've tried your suggestion. I've made an index file with my oxygen (O) and my hydroxyl group (OH). Here my results: H-bond average (calculated using num.xvg): O = 1.10 +/- 0.62 OH = 2.06 +/- 0.66 (The first line from .log for each group) # Donor Hydrogen Acceptor O = SOL2OW SOL2HW1 MET1O OH = MET1O MET1HH SOL2OW My command line for each group was: gmx_507 hbond -s met.SIM.tpr -f met.SIM-traj.xtc -n wat_ana.ndx -shell 0.5 -r 0.35 -a 30 -num met.num.xvg -hbn met.hbn.ndx -don met.donors.xvg -dan met.dan.xvg -g met.log So I am a bit confused. I was expecting only 1 H-bond from OH group (since O is able to donate only one H), and 2 H-bonds accepted for O. Based on the .log, gmx hbond doesn't seem to be calculating H-bond for acceptors and donors at the same time, what would justify this value of 2 for OH (1 accepted and 1 donated). So, I ran out of ideas. Does anyone have any? Does these values make sense? Cheers! Marcelo ------------------------------ > > Message: 2 > Date: Mon, 14 Aug 2017 12:13:38 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Donors and Acceptors - gmx hbond > Message-ID: > <CAMNuMAQ2LLXpSQ1ChMoKiBd-YJP4s+76Dou0Wvn5sLmj_UGJng@ > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > I would use the selection groups judiciously, for example have one of them > with only donor atoms in it. > > Mark > > -- -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- 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.
