[gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67

Marcelo Depólo marcelodepolo at gmail.com
Mon Aug 14 15:51:58 CEST 2017

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?


> Message: 2
> Date: Mon, 14 Aug 2017 12:13:38 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at 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

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